To amplify grain production capacity, a global trend is emerging in which many regions are transitioning from dependence on rainfall to irrigated agriculture. An illustrative example of this form of land consolidation is the conversion from dryland to paddy fields, which has changed the ecological environment of farmlands, resulting in significant effects on carbon fixation and emissions. However, there currently exists a deficiency in essential understanding regarding the short-term effects of dryland-to-paddy conversion on ecological processes tied to soil carbon-fixation bacteria and carbon emission efficiency (CEE). Therefore, field monitoring and high-throughput sequencing were carried out to monitor the changes in soil carbon emission efficiency and carbon-fixation bacteria before and after the conversion. Our results indicate that while conversion from dryland to paddy fields can boost grain yield, it also results in an increase in soil carbon emissions and a consequent decrease of 25.78% in carbon emission efficiency. This transition has resulted in an increased soil carbon-fixing bacterial alpha diversity index and enhanced network complexity. The structural equation model indicates that changes in soil environmental factors, especially soil moisture, soil organic carbon (SOC), readily oxidizable carbon (ROC), and carbon-fixing bacteria, are the primary drivers of CEE variation (p < 0.05). Given the critical role that the soil carbon cycle plays in global climate change, there is a pressing need for increased global attention towards the carbon emissions triggered by the transition from rainfed to irrigated agriculture.