Low-carbon agricultural practices have received increasing attention, and the rapid development of agricultural product quality certification in China has provided a potential way to implement low-carbon agriculture. This study employs an endogenous switching regession to examine the effects of quality certification on low-carbon production behaviors using the survey data of 1,042 rice farmers in Hubei Province, China. The empirical results show that, first, the quality certification participation has a positive and statistically significant impact on farmers’ low-carbon production behaviors. In particular, the treatment effect of quality certification participation is to increase farmers’ low-carbon production level to appropriately 71.85%. Second, a disaggregated analysis by quality certification type reveals no significant difference between public geographical indication certification and private green food and organic product certification in promoting farmers’ low-carbon production behaviors. Nevertheless, the effect of multiple certifications on low-carbon production behaviors is significantly stronger than that of single certification. Third, disaggregated analysis indicates that new agricultural business entities are more likely to implement low-carbon production after participating in quality certification than traditional farmers.