In this paper, the ratio of gross agricultural production (GAP) and agricultural carbon emission is defined as agricultural carbon emission efficiency (ACEE). Considering rural labor transfer (RLT) increases the agricultural machinery intensity (AMI), the two are substitutes for each other and may interact with agricultural carbon emission efficiency (ACEE), we constructed a Simultaneous Equations Model (SEM) of ACEE, RLT and AMI, and analyzed the interaction mechanism of these three variables by using the Three-Stage Least Squares (3SLS) method to solve the endogeneity of the model. The following conclusions are drawn. First, RLT and AMI significantly promote the improvement of ACEE, while the improvement of ACEE and AMI further promotes RLT. Secondly, the causal relationship and influence mechanism of ACEE, RLT and AMI are interactive and multi-directional. An increase in AMI promotes ACEE, but an increase in ACEE inhibits an increase in AMI, suggesting that the marginal rate of substitution of machinery for labor is decreasing. Finally, China has significant regional heterogeneity. Labor transfer and machinery are only direct factors in increasing ACEE, while factors such as economic base, technology level and farmers' attitudes provide environmental support for the effective improvement of ACEE.