Using the detailed field experiment data from 1981 to 2009 at four representative agro-meteorological experiment stations in China, along with the Agricultural Production System Simulator (APSIM) rice-wheat model, we evaluated the impact of sowing/transplanting date on phenology and yield of rice-wheat rotation system (RWRS). We also disentangled the contributions of climate change, modern cultivars, sowing/transplanting density and fertilization management, as well as changes in each climate variables, to yield change in RWRS, in the past three decades. We found that change in sowing/transplanting date did not significantly affect rice and wheat yield in RWRS, although alleviated the negative impact of climate change to some extent. From 1981 to 2009, climate change jointly caused rice and wheat yield change by −17.4 to 1.5 %, of which increase in temperature reduced yield by 0.0–5.8 % and decrease in solar radiation reduced it by 1.5–8.7 %. Cultivars renewal, modern sowing/transplanting density and fertilization management contributed to yield change by 14.4–27.2, −4.7– −0.1 and 2.3–22.2 %, respectively. Our findings highlight that modern cultivars and agronomic management compensated the negative impacts of climate change and played key roles in yield increase in the past three decades.