The coordinated development of the economy, resources, and environment is a key aspect of sustainable development. China’s rapid agricultural modernization has been accompanied by the continuous growth of rural economic aggregate and carbon emissions from the planting industry. However, the quantitative relationship between these two factors and its internal mechanism are not yet fully understood. In this paper, the Intergovernmental Panel on Climate Change (IPCC) method is used to calculate the carbon emissions of the planting industry in China from 1998–2019. Based on this, the Tapio decoupling analysis model was constructed to study the decoupling relationship between economic development and carbon emissions of the planting industry in China from 1998–2019 and the associated spatial and temporal evolution patterns. The effect of the complete decomposition model (without residuals), in terms of carbon emissions from the planting industry, on the process of economic development and its transmission mechanism are introduced. The results show that: (1) The carbon emissions of the planting industry in China increased with the economic development occurring from 1998–2005, where agricultural economic development was highly dependent on resource factors and the environment. The growth trend of carbon emissions of the planting industry slowed from 2006 to 2019, while economic development has gradually realized the decoupling of carbon emissions from the planting industry. (2) From 1998–2019, in Heilongjiang, Sichuan, and Hunan, the economic development was given priority, showing strong and negative decoupling with carbon emissions from farming. The economic development in most regions were given priority, showing strong decoupling with carbon emissions from farming. Up to 2019, decoupling was observed with a significant trend of spatial agglomeration. (3) Economic scale effects had a positive influence on the carbon emissions of the planting industry, while the technology effect and population effect had an inhibiting influence on the carbon emissions of the planting industry. The key policy implication of this paper is that improvement of the quality of economic development serves as the premise for the transformation of the economic development mode. It is necessary to reasonably regulate the economic growth rate and expansion scale, reduce resource consumption and pollutant emission technology, and to make full use of resources, in order to provide a basis for the formulation of reasonable emission reduction policies. An effective way to realize the sustainable development of the agricultural economy would be to improve the technical efficiency, control the population scale appropriately, and optimize the agricultural industrial structure.