Return of crop residues directly as straw, animal manure, or biochar are recommended management options for biowaste recycling and soil organic carbon (SOC) maintenance in agriculture. However, to address the soil health challenges associated with soil degradation and climate change, it is critical to determine if or which of these different forms of crop residues could deliver a synergic improvement in SOC storage, emission reduction, and crop productivity following field application. In this study, maize straw in the form of air‐dried biomass (CS), manure via cattle digestion (CM), and biochar via pyrolysis (CB) was respectively amended once at a dose of 10 t C ha−1, in comparison to no maize straw addition (CK), in a paddy field under rice‐wheat rotation. Changes in soil properties, SOC storage, greenhouse gas (GHG) emissions, and rice/wheat yield were examined over two consecutive rice/wheat rotation cycles following soil amendment. The total rice grain yield considerably increased by 6% under CM and CB, while it reduced by 6% under CS compared to CK. Soil nutrient content persistently increased under CM and CB by 4.2% ~ 17% and 11% ~ 26% for total nitrogen, 26% ~ 61% and 20% ~ 53% for available P, and 2% ~ 82% and 30% ~ 115% for available K, respectively. Topsoil SOC storage increased considerably by 8% under CM and 20% under CB, while remained unchanged under CS, compared to CK. The total methane (CH4) and nitrous oxide (N2O) emissions were considerably increased by 7 folds and 15% under CS and 3.5 folds and 61% under CM, respectively, compared to CK. In contrast, these emissions considerably decreased under CB by 33% for CH4 and 29% for N2O. Consequently, the C emission efficiency considerably reduced under CS and CM but increased under CB over the two rotation cycles monitored. Moreover, the soil quality index (SQI) considerably improved under CM and CB but remained unchanged under CS compared to CK. Among the different forms of straw return, manure, and biochar, straw amendments differed considerably in their effects on C sequestration, GHG emissions, and crop productivity. Only biochar from crop residues synergistically improved these functions in the short‐term following application to paddy soil.