Following climate change, changes in precipitation patterns and food security are major challenges faced by humans. However, research on how these changes in precipitation pattern impacts food supply is limited. This study aims to elucidate this impact and response mechanisms using precipitation data of a climate change-sensitive confluence zone of the southwest and southeast monsoons in Yunnan Province from 1988 to 2018. The results revealed that the precipitation pattern could be divided into three periods: abundant precipitation (Stage I, from 1988 to 2004), decreased precipitation (Stage II, from 2005 to 2015), and drought recovery (Stage III, from 2016 to 2018). Following the transition from Stage I to Stage II and from Stage II to Stage III, the area of precipitation changed significantly, accounting for 15.07%, 13.87%, and 16.53% of Yunnan’s total area, for Stages I, II, and III, respectively. At the provincial level, a significant positive correlation was observed between precipitation and food production (r = 0.535, P < 0.01), and the correlation coefficient between precipitation and grain yield was higher than that between precipitation and meat and milk production. Based on a precipitation-grain yield transect and breakpoint detection method, key precipitation thresholds affecting grain yield were estimated as 700 and 1500 mm, respectively; when precipitation was < 700, 700-1500, and ≥1500 mm, the correlation coefficients between precipitation and grain yield were 0.448 (P < 0.01), 0.370 (P < 0.01), and -0.229 (P > 0.05), respectively. Based on the precipitation thresholds, Yunnan Province can be divided into precipitation surplus, precipitation equilibrium, and precipitation deficit regions, corresponding countermeasures to stabilize grain yield were proposed for each of these regions. The threshold effect of precipitation on grain yield is controlled by molecular-level water-crop mechanisms, in which reactive oxygen species, a by-product of plant aerobic metabolism, plays a key regulatory role.