The contradiction between rapid soil degradation and increased food demand is becoming increasingly prominent. Reasonable recycling of agricultural waste can affect soil productivity and environmental health, thus playing a crucial role in the sustainability of agricultural production. Through a meta-analysis of 160 studies in the region of upland double cropping in China, we evaluate crop yield and soil quality responses to organic amendments. Results indicated that soil quality index (17.6%–26.3%) and crop yield (6.0%–9.0%) were significantly increased by adding organic amendments to chemical fertilizer. Combination of organic materials with total chemical fertilizer (OTC) and with part chemical fertilizer (ORC) significantly increased the yield by 8.3% and 8.7% and soil quality by19.5% and 18.4%, respectively. However, application of organic materials alone (O) decreased yields (by −0.6%), but significantly increased soil quality (by 49.1%). On average, organic amendments resulted in higher crop yield and soil quality index, despite variability introduced by tillage regimes and conditions of soil and climate. Relatively larger positive effect in crop yield and soil quality occurred with mean annual precipitation >1000 and <600 mm, respectively. Additional analyses found that biochar, organic fertilizer or ORC can promote sustainable agricultural development via improving crop yields, soil quality, and reducing nitrogen losses. Our results provide the first systematic review of effect of the organic amendments on the balance between soil quality and crop yield. The findings suggest that impacts of adding organic amendments to chemical fertilizer may be used as the foundation for policies. However, the combined use of organic amendments and other farmland management practices still present an area that needs further research in order to promote sustainable development of agriculture.