Abstract: The utilization efficiency of water resources needs to be quantify the contribution in grain production systems in water-scarce areas, in order to implement the water resources management. In this study, the water footprint and emergy analysis were combined to construct an evaluation index system of water resources emergy (water resources emergy input, contribution ratio and use efficiency, which were specifically divided into total, blue and green water). The wheat and maize production systems were taken as the study area along the Yellow River Basin from 2001 to 2016. The blue and green water footprints were also introduced in the emergy analysis of water resources in crop production system during the actual water consumption from the perspective of emergy. As such, the blue and green water resources were distinguished to quantify the temporal and spatial evolution of emergy input, contribution ratio, and use efficiency of water resources in grain production systems along the Yellow River Basin. The results showed that the proportion of renewable emergy flow was less than 30% annually in the total emergy input of wheat and maize production system in the nine provinces along the Yellow River, where water resource was the largest input in the renewable resources. The emergy input of water resources increased more outstandingly in maize production system, compared with the wheat. The emergy input of total, blue and green water increased by 59.69%, 27.77% and 118.14%, respectively. The maximum annual average values for the total water emergy input of wheat and maize were distributed in Henan and Inner Mongolia, respectively, which was 26.86 times and 175.95 times of the minimum value in Qinghai. Furthermore, the annual average contribution ratios of blue water (i.e., surface and groundwater) emergy were 1.90 times and 1.26 times higher than those of green water in wheat and maize production system. There was the similar trend in the emergy contribution ratios of blue and green water in wheat, whereas the opposite trend was found in corn, where the difference decreased from 5.26% to 0.61%. The maximum contribution ratios of water resources emergy in wheat and maize were distributed in the three provinces of northwest China (Qinghai, Ningxia, and Inner Mongolia). The annual average of the blue water emergy contribution ratio was higher than that of green water in wheat production systems, except Qinghai. The total use efficiencies of water emergy increased by 38.83% and 39.95% in the wheat and maize production systems, respectively. There was small inter-annual change of the blue water emergy use efficiency, whereas, the green water showed an upward trend, much higher than that the blue water. There was a still different distribution in the utilization degree of blue and green water resources among provinces. Henan and Shandong shared the maximum annual average of total water emergy use efficiency in the wheat and maize production systems, respectively. Consequently, there was significantly improved emergy utilization efficiency of water resources during the study period. The findings can provide a strong reference to evaluate the water resource efficiency for the optimal allocation of agricultural production along the Yellow River Basin.