The long-term field experiment data at four representative agro-meteorological stations, together with a crop simulation model, were used to disentangle the contributions of climate change, variety renewal, and fertilization management to rice yield change in the past three decades. We found that during 1981–2009 varieties renewal increased rice yield by 16%–52%, management improvement increased yield by 0–16%, and the contributions of climate change to rice yield varied from −16% to 10%. Varieties renewal and management improvement offset the negative impacts of climate change on rice production. Among the major climate variables, decreases in solar radiation reduced rice yield on average by 0.1% per year. The impact of temperature change had an explicit spatial pattern. It increased yield by 0.04%–0.4% per year for single rice at Xinbin and Ganyu station and for late rice at Tongcheng station, by contrast reduced yield by 0.2%–0.4% per year for single rice at Mianyang station and early rice at Tongcheng station. During 1981–2009, rice varieties renewal was characterized by increases in thermal requirements, grain number per spike and harvest index. The new varieties were less sensitive to climate change than old ones. The development of high thermal requirements, high yield potential and heat tolerant rice varieties, together with improvement of agronomic management, should be encouraged to meet the challenges of climate change and increasing food demand in future.