With increasing application of nitrogen (N), phosphorus (P), and potassium (K) fertilizers, especially in China’s fruit crops, the agronomic responses of fruit crops to fertilization may be reduced with time. Thus, the quantification of these responses would be useful for establishing nutrient recommendation and fertilizer management for fruit crops. Here, a meta-analysis including 552 paired data for agronomic response and 1283 sets for amounts of optimal fertilization from 293 field studies in China were performed to systemically quantify these variations of yield response (YR), relative yield (RY), agronomic efficiency (AE), and partial factor productivity (PFP) in response to the application of N, P, or K fertilizer under different groups including fruit crop types, time, and regions. The results showed that the average YRs to N, P or K fertilizer were 7.6, 5.2, or 5.9 t ha−1
, indicating related RYs of 78.0%, 82.9%, or 82.4%, respectively. All of the RYs for N, P, or K application in studies after 2000 were higher and less variable than those before 2000. Higher RYs were also shown for deciduous fruit trees when compared with evergreen fruit trees. The average AEs of N, P, and K fertilizer in China’s fruit crops were 29.1, 32.4 and 20.2 kg kg−1
, all of them were negatively correlated with fertilizer rate. Due to a higher yield response and less fertilizer rate, annual crops (mainly watermelon and melons) had significantly higher AE than that of perennial crops. The average PFPs of N, P, and K fertilizer in China’s fruit crops were 129, 205, and 113 kg kg−1
, all of which showed a declining trend with time. These findings demonstrated that the building-up of soil indigenous nutrient supply (indicated by RY) together with improving fruit varieties, as well as pest management and other forms of management could make external fertilization less important for increasing the yield of fruit crops in China. A rational nutrient management is therefore crucial for balancing yield and environmental concerns in countries like China, India, and other countries where fertilizers are often overused.