Abstract: Energy consumption and carbon emissions from all sectors have increased over the past four decades. Climate change caused by carbon emissions from energy activities poses a serious risk to humans. Although carbon emissions from the direct energy consumption of agriculture are limited, agricultural production modes and consumption patterns are undergoing significant changes. The extension of the supply chain has resulted in an increase in energy consumption and carbon emissions. To estimate the carbon emissions from agrifood systems, this study used the input-output tables from 1997 to 2018 and the data of energy consumption by sector in China to estimate the carbon emissions and analyze its trends, components, and characteristics based on the input-output model. The most prominent advantage of this model is that it not only captures the carbon emissions from direct energy use, but also includes the carbon emissions from indirect energy use due to the production of intermediate inputs. This study had several findings. First, with China’s economic development, total energy consumption increased 2.2 times from 1.5 billion tons in 2000 to 4.7 billion tons of standard coal in 2018. The energy consumption of the agriculture and food processing industry has increased from 42.3 million tons and 39.2 million tons of standard coal in 2000 to 87.8 million tons and 75.1 million tons of standard coal in 2018, respectively. Second, carbon emissions from energy use in agrifood systems and non-agrifood systems have increased from 530.0 million tons and 2.7 billion tons in 1997 to 670.0 million and 9.7 billion tons in 2018, respectively. However, the growth rate of agrifood systems (1.1%) was much lower than that of non-agrifood systems (6.3%); therefore, the share of agrifood systems in the total carbon emissions from energy use declined from 16.3% in 1997 to 6.4% in 2018. Third, the food processing industry’s carbon emissions have increased significantly and have become the most important carbon emission source in agrifood systems, with 420.0 million tons accounting for 62.7% of the carbon emissions from energy activities in the agrifood systems in 2018. Carbon emissions from agriculture-related transportation and storage, wholesale and retail, and catering have continued to rise. In 2018, the total carbon emissions were 73.58 million tons, contributing to 11.1% of the carbon emissions of the energy activities in the agrifood systems. The carbon emissions from agricultural energy use showed a downward trend owing to the improvement in energy efficiency; however, this was still the second largest carbon emission source. The carbon emissions in 2018 were 170 million tons, accounting for 26.2% of the carbon emissions from energy activities in agrifood systems. Based on these results, policy suggestions are provided, such as reducing emissions from the supply chain, accelerating the development of low carbon emissions and low energy consumption in the food processing industry, promoting agricultural green development, and optimizing the energy structure to help to reduce carbon emissions.