<p>Southern China has been the most important economic and population center in the country for the past thousand years. However, in the study of the impact chain of “historical climate change-agricultural harvest-society consequence,” the relationship between climate change and agricultural harvest in southern China remains unanswered. In this study, the Ming and Qing dynasties (1368–1911CE) with abundant historical records were used to reconstruct the annual harvest index sequences of nine representative subregions in southern China, and their response patterns to temperature and precipitation changes were analyzed. Although southern China has relatively abundant water and heat resources, the results showed an overall correlation between agricultural harvesting, temperature, and precipitation, with warmer and wetter climates resulting in better harvests. However, there are also some regional characteristics. Agricultural harvest and temperature changes in the middle and lower reaches of the Yangtze River have significant correlations at the interannual and decadal scales, whereas there is no significant correlation between agricultural harvest and temperature changes in Chuanyu and south China. Precipitation has a more widespread impact on agricultural harvests in southern China than temperature change. The sensitivity of agricultural harvests in southern China to temperature and precipitation was generally weaker than that in northern China. Moreover, after the 1720s, the sensitivity of agricultural harvests in southern China to changes in temperature and precipitation decreased, and the resilience of agricultural production to climate improved. This change may have had different effects on the mechanisms of climate impact on society between the Ming and Qing dynasties.</p>