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Climate is the most important environmental factor influencing yield during rice growth and development. To investigate the relationships between climate and yield under different crop rotation patterns and planting methods, three typical rotation patterns (vegetable–rice (V), rape–rice (R), and wheat–rice (W)) and two mechanical planting methods (mechanical transplanting (T1) and mechanical direct seeding (T2)) were established. The results showed that compared to the V rotation pattern, the average daily temperature (ADT) during the sowing to heading stage increased under both R and W rotation patterns, which significantly shortened the growth period. Thus, the effective accumulated temperature (EAT), photosynthetic capacity, effective panicle (EP), and spikelet per panicle (SP) under R and W rotation patterns significantly decreased, leading to reductions in grain yield (GY). VT2 had a higher ratio of productive tillers (RPT), relative chlorophyll content (SPAD), leaf area index (LAI), and net photosynthetic rate (Pn) than those of VT1, which significantly increased panicle dry matter accumulation (DMA), resulting in an increase in GY. Although RT2 and WT2 had a higher RPT than those of RT1 and WT1, the GY of RT1 and WT1 decreased due to the significant reductions in EAT and photosynthetic capacity. Principal component analysis (PCA) showed that the comprehensive score for different rotation patterns followed the order of V > R > T with VT2 ranking first. The structural equation model (SEM) showed that EAT and ADT were the most important climate factors affecting yield, with total effects of 0.520 and −0.446, respectively. In conclusion, mechanical direct seeding under vegetable–rice rotation pattern and mechanical transplanting under rape–rice or wheat–rice rotation pattern were the rice-planting methods that optimized the climate resources in southwest China. [ABSTRACT FROM AUTHOR]