Drip fertigation with reduced fertilizer and water inputs has been widely used in greenhouse vegetable production in China. However, farmers usually do not apply additional organic material with a high carbon content, although soil organic carbon (SOC) concentrations are mostly below the optimum level for vegetable production. Returning straw or biochar to fields is an effective strategy for sustainability and environmental friendliness. We tested whether drip fertigation, (DIF) combined with maize straw (DIF+S) or biochar (DIF+BC), is a suitable option to improve SOC sequestration over eight growing seasons, and how these options affect soil N2O emissions and yields or partial factor productivity of applied N (PFPN) of crops over three growing seasons. During the winter–spring growing season, DIF+BC significantly reduced soil N2O emission by 61.2% and yield-scaled N2O emission by 62.4%, while increasing the tomato yield and PFPN compared with DIF. Straw incorporation had similar trends but without significant effects. Conversely, straw and biochar incorporation increased N2O emission during the autumn–winter season. The structural equation model indicated N2O emission was dominantly driven by soil NH4+-N concentration, temperature and moisture. The N2O emission factor decreased significantly with increased PFPN. Moreover, the contribution of biochar to the increased SOC was approximately 78%, which was four times higher than that of straw incorporation. Overall, the results highlighted the potential of drip fertigation with biochar incorporation to mitigate N2O emissions, improve PFPN and significantly increase SOC storage, which could all contribute to maintaining environmental sustainability and soil quality of greenhouse vegetable production.