Inclusion of cover crops (CCs) in cropping systems can improve soil quality, reduce agricultural inputs, and improve environmental sustainability. While CCs have been widely promoted in China in recent years, a quantitative assessment of CC effect on crop yield across China is lacking. There is also no overarching analysis on factors explaining variation in yield effects. Here, we carried out a meta-analysis to evaluate the effects of CCs on subsequent primary crop yield in China, based on 53 published studies reporting 442 yield ratios with and without CCs. We found that CCs increased subsequent primary crop yields by 9.7 % on average when compared with fallow across China. The effects of CC varied with different factors related to climatic zone, field management and soil properties. CC type (legume or not), CC season (growing in winter or summer) and nitrogen input were factors substantially influencing primary crop yield. We identified high yield benefits in subtropical rice systems with winter CCs (12.9 ± 3.9 %) but no significant yield benefits in temperate wheat systems with summer CCs (1.9 ± 6.6 %). Within subtropical rice systems, both legume and non-legume CCs were tested widely, and the effects of legume CCs (14.6 ± 4.0 %) on primary crop yield were greater than those of non-legume CCs (7.9 ± 3.7 %). The yield benefits of CCs decreased with increasing fertilizer inputs. These results may be used for developing policy recommendations to improve primary crop yield by integrating targeted CCs associated with nitrogen management into cropping systems in China.