Based on the analysis of the theoretical connotation of high-quality agricultural development, this paper constructed a comprehensive evaluation index system of high-quality agricultural development from two dimensions of natural environment and social economy. The level of high-quality agricultural development of each county was measured using the panel data of 183 counties in Sichuan Province from 2000 to 2020. At the same time, the spatial and temporal evolution of the agricultural high quality level of the natural system, the socioeconomic system and the integrated system in these counties was explored. The trade-off model in management was improved to calculate the degree of coupling coordination of natural and socioeconomic systems, which quantified the coupling level between different subsystems in the process of high-quality agricultural development. The results showed that: (1) The comprehensive index of high-quality agricultural development in Sichuan Province experienced a period of volatility (2000-2011) and a period of rapid growth (2011-2020). In this process, the natural dimension index was higher than the socio-economic dimension index on the whole, but at the same time, the former also showed stronger instability. (2) The high value of agricultural quality development level was concentrated in Chengdu Plain, its surrounding hilly areas and a few counties in southern Sichuan. From these two high-value centers to the periphery of the study area, the high quality level gradually declined. Compared with the vast plain and hilly areas, the high quality development level of northwest Sichuan Plateau was still relatively lagging behind. (3) Under the complex interaction between the natural and socio-economic system, the high-quality development of Sichuan agriculture realized the transformation from the low-value uncoordinated stage to the low-value uncoordinated stage, and then to the high-value uncoordinated stage. There were significant differences in the coupling uncoordinated regions during the aforementioned periods, and these regions were facing different shortcomings of high-quality agricultural development. (4) There was a complex interaction relationship between the natural and socio-economic indices of high-quality agricultural development. This relationship was significantly related to the terrain, especially in mountainous counties.