As an important factor affecting ecological sustainability, the food industry’s ecological efficiency (EE) deserves great attention and control. In 2013, China implemented a carbon emissions trading policy (CETP) to limit carbon emissions from various industries to promote the optimization of the ecological environment. To explore the ecological sustainability of China’s food industry, identify the factors affecting the EE of the food industry, and study the influence heterogeneity and influencing mechanisms, the impact of the CETP on the food industry, which emits high volumes of greenhouse gasses, requires evaluation. Many scholars have studied the policy’s effect from the perspective of EE, but they have ignored the food industry, which is the main carbon emitting sector, and there is a lack of heterogeneity analyses of the influencing factors. This study reviewed the implementation process and characteristics of the CETP in the past decades. Using provincial panel data from 2003 to 2019, this study measured the EE in the food industry through the difference-in-difference model, evaluated the emission reduction and economic effects of the CETP on the food industry, characterized the heterogeneity of the policy’s effectiveness, and analysed its mechanism using three-stage mediating regression. The results showed that (1) the CETP significantly affected the food industry’s EE, which increased by 38.3% on average in experimental provinces compared with non-experimental provinces. (2) For the food industry, the policy’s effect was most significant in the food manufacturing and tobacco subsectors, and these subsectors in the experimental provinces increased by 66.0% and 39.7%, respectively; meanwhile, the policy’s effect was not significant in agriculture and subsidiary food processing and beverage manufacturing. By industrial area, the policy’s effects were significantly higher in the eastern region compared with the central and western regions. The influence on the food industry’s EE in the eastern region was close to 150%, while in the central and western regions, it was not significant. (3) The CETP promoted the food industry’s EE by improving energy consumption structure and technological innovation. The proportion of coal consumption decreased by 6.34% on average, and the technological innovation level increased by 25.1% on average in the experimental provinces’ food industries. The research findings indicate that the CEPT is a good practice and worth spreading. For food industry enterprises with high carbon emissions, attention should be paid to low-carbon transformation through technological upgrading and management optimization. For policymakers, targeted policies are needed to establish a national unified carbon trading market so that the national carbon emissions can be controlled, and the gap between regional carbon emissions can be narrowed.