Abstract: Farmland use transition is often required in sustainable agriculture. An important path can be expected to balance the farmland use transition and eco-efficiency, in order to promote urban-rural integration. This study aims to explore the impact of the farmland use transition on the farmland use eco-efficiency and threshold effect in the Chengdu-Chongqing pilot Zone. The research area was taken from the national coordinated urban-rural comprehensive supporting reform pilot areas. The panel data were collected from the Chengdu-Chongqing pilot Zone from 2005 to 2022. Projection pursuit method based on sparrow search algorithm (SSA-PPM), super-efficiency SBM, Panel Quantile, and the threshold regression model were utilized to explore the impact of the farmland use transition on the farmland use eco-efficiency. The results found that: 1) The farmland use transition generally shared a fluctuating downward trend from 2005 to 2022, with the average decrease from 1.633 to 1.536. Meanwhile, the farmland use eco-efficiency exhibited an overall upward trend, with the average value rising from 0.688 to 0.711. The overall eco-efficiency value remained below 1. Data Envelopment Analysis (DEA) results indicate that there was a relative inefficiency in the losses in the farmland use eco-efficiency. However, the number of DEA-efficient counties shared an upward trend, increasing from 4 in 2005 to 8 in 2022. Spatially, both the farmland use transition and eco-efficiency exhibited the zoned differentiation pattern of “low-to-medium efficiency in the center and high efficiency at the periphery.” High-value counties and districts were concentrated in areas rich in arable land resources surrounding, such as Tongnan, Hechuan, Tongliang, Jintang, and Jianyang. 2) The farmland use transition, along with its explicit and implicit transformations, also demonstrated a significant positive impact on the eco-efficiency, with the coefficients all exceeding 0.5. The transition of the arable land utilization significantly enhanced the eco-efficiency, with the impact coefficients ranging from 0.532 to 0.585 across low to high quantiles. There were positive effects on the eco-efficiency in the study area and parts of Chengdu, with the strongest positive impacts under high quantile conditions, including the quantitative transition, spatial structure transition, production and ecological function transition of the arable farmland. In the Chongqing portion, there was a monotonic decrease in the regression coefficients for the spatial structure and production function transition, particularly with the increasing quantiles. However, more pronounced latent and explicit transitions were observed in the arable farmland use in both Chengdu and Chongqing, due to the arable land resource conditions and topography. 3) There was a moderate influence of the farmland use transition on the farmland use eco-efficiency. The dual threshold effect of the urbanization level was presented with the threshold values of 0.361 and 0.751, respectively. In Chongqing and Chengdu, the positive impact of the farmland use transition on the eco-efficiency first declined and then increased as the urbanization levels continued. In the Chongqing part, it was moderated by the single threshold effect of the financial support for agriculture, with a threshold value of 0.398. The farmland use transition on the eco-efficiency was nonlinearly weakening. The findings can provide a scientific basis to effectively enhance the regional farmland use transition and eco-efficiency. Scientific guidance can also be offered for the regional urban-rural integration and green development.