To promote the modernization of agriculture and rural areas in Chongqing, using 29 districts and counties in Chongqing, excluding the central urban area, as the research area, an evaluation index system for agricultural transformation and development in the research area was constructed from four dimensions: agricultural production entities, agricultural production levels, agricultural inputs, and agricultural industrialization. The spatiotemporal evolution and obstacle factors of agricultural transformation and development in the research area and counties from 2011 to 2020 were analyzed using entropy weight method, TOPSIS method, spatial autocorrelation analysis, and obstacle model. The overall level of agricultural transformation and development in the research area and counties showed an upward trend from 2011 to 2020. The average value of the comprehensive evaluation index for agricultural transformation and development in each area and county increased from 0.260 6 in 2011 to 0.432 2 in 2020. Moreover, the process of agricultural transformation and development in the research area and counties went through three stages: preliminary development, gradual development, and rapid development. The area with the highest level of agricultural transformation and development in the research area is the Yuxi area, followed by the Yudong area, the southeast area, and the northeast area. The proportion of counties with high-level agricultural transformation and development has increased from 10.3% to 24.1%. There is a strong global autocorrelation in the transformation and development of agriculture in the research area. The “high high” agglomeration area is mainly located in the western part of Chongqing, while the “low low” agglomeration area is mainly located in the northeastern part of Chongqing. From a larger perspective, the main obstacles to the transformation and development of county-level agriculture in the western and eastern regions of Chongqing are agricultural industrialization and agricultural investment, while the main obstacles to the transformation and development of county-level agriculture in the southeastern and northeastern regions of Chongqing are agricultural production level and agricultural production entities. From the perspective of specific evaluation indicators, rural per capita electricity consumption, rural tourism development, and per capita agricultural, forestry, animal husbandry, and fishery output value are the three main obstacles to the transformation and development of agriculture in the research area. The above results indicate that from 2011 to 2020, the spatial and temporal differences in the level of agricultural transformation and development and the regional differences in the obstacles to agricultural transformation and development in the study area were relatively significant.