Agriculture is the link between sustainable development and human nutrition and health. Increasing carbon emissions from agriculture threaten ecosystems and human living conditions. However, the level of agricultural emissions in China and uncertainties in the global supply chain limit the implementation of more sustainable agricultural policies in China. This paper aims to assess the environmental impacts of Chinese agriculture from the perspective of consumption carbon emissions. This paper adopts a multi-regional environmental input-output model, uses the global supply chain to identify major trade partners and key industries, and estimates China’s domestic agricultural carbon emissions from the perspective of intermediate product input industries. Then, from the perspective of the country (region) and intermediate product input industry, we estimate the embodied carbon of China’s agriculture in international trade. Finally, based on the structural decomposition analysis, we factor out the changes in carbon emissions embodied in Chinese agriculture from the demand and supply sides. The findings underscore that energy supply, crop cultivation, livestock farming, machinery and equipment manufacturing, food production, and electrical equipment manufacturing are the primary drivers behind the growth in carbon emissions. According to the SDA decomposition results of the global supply chain, the major partners of China’s agricultural sector, which are also the top ten carbon emission sources, can be roughly divided into four categories: developed countries with a long geographical distance from China, BRIC countries, Asian neighbors and Taiwan region. The results of the factor decomposition analysis reveal that the surge in carbon emissions is primarily attributable to increased demand and decreased production emission efficiency. In contrast, advancements in industry-wide technology play a key role in reducing carbon emissions. Conclusively, this study provides scientific basis and policy recommendations for formulating sustainable agricultural development strategies and protecting the ecological environment, which is expected to provide an important reference for solving the problem of global climate change.