Abstract: Abstract: Various production and living activities have posed a great impact on the natural environment in the era of ecological civilization. It is necessary to consider how to implement nature restoration and protect while taking from it. Most studies and state-of-art technologies have been developed for resourceful recycling of agricultural wastes, with emphasis on the modern biotechnology and engineering to enhance microbial reduction. This recycling allows for the timely replenishment of nutrients that consumed by the plant production, while reducing the use of chemical fertilizers and fossil fuels. We need to bring ecological balance back. This change of concept fully reflects the evolution of human civilization, where the construction of ecological civilization is highly demanding. Correspondingly, the agricultural engineering discipline is directly related to agricultural ecology and environment, thereby also needs to raise the height of understanding in theory. The scientific ethical concept of harmonious coexistence can be emphasized between human and water, soil, green and resources utilization. A discipline standard can also be recognized as the protection of natural environment and the maintenance of ecological balance. Therefore, the main purpose of agricultural engineering discipline has been changed to promote the harmonious coexistence between human and nature. Chinese cultural factors are also precisely integrating to one of the most important part of agricultural engineering. Consequently, the discipline of agricultural engineering should develop the agricultural production and economy under the premise of respecting and maintaining the natural environment. At the same time, the agricultural development needs to focus on some factors between human and nature, such as agroecology and agricultural culture. The research focus of agricultural development can be extended from a single element of survival to three elements of production, life and ecology. As such, the agricultural engineering discipline in the era of ecological civilization is facing new opportunities and challenges. In this study, a new connotation of agricultural engineering discipline was proposed according to the new ideas and requirements of ecological civilization, including the research objects, theoretical systems, and research of agricultural engineering disciplines. Specifically, the object of study in the discipline of agricultural engineering can be taken the ecosystem, consisting of human and agricultural resources, production and consumption in the era of ecological civilization. It has expanded from agricultural biological systems to agricultural ecosystems. The theoretical system has incorporated the concepts of ecological civilization and agricultural culture. The scientific research has been supplemented to strengthen the cutting-edge fields, such as system science, numerical simulation, big data, and cloud computing. The agricultural engineer in the era of ecological civilization is no longer simply a designer or producer of agricultural machinery and equipment, or a developer of agricultural energy, or a manager of agricultural water and soil. In essence, a modern agricultural engineer has become a farm planner to manage the various risks encountered in agricultural production, particularly integrating agricultural equipment, environment, resources, culture, and production factors. In addition, a future direction was addressed for the construction of agricultural engineering discipline using some examples from the international exploration and application. The results demonstrated that the needs of social progress was met in the development concept of the new connotation of agricultural engineering discipline in the era of ecological civilization. The finding can provide a promising scientific reference to further enrich the theoretical system of agricultural engineering disciplines, while a potential technical support to the ethical form of agricultural culture for sustained social prosperity. Consequently, the agricultural engineering discipline can be expected to become a scientific driving force for the advance of harmonious coexistence, virtuous cycle, and comprehensive development of human, nature and society.