Scientific analysis of regional agricultural carbon emission prediction models and empirical studies are of great practical significance to the realization of low-carbon agriculture, which can help revitalize and build up ecological and beautiful countryside in China. This paper takes agriculture in Guangdong Province, China, as the research object, and uses the extended STIPAT model to construct an indicator system for the factors influencing agricultural carbon emissions in Guangdong. Based on this system, a combined Isomap–ACO–ET prediction model combing the isometric mapping algorithm (Isomap), ant colony algorithm (ACO) and extreme random tree algorithm (ET) was used to predict agriculture carbon emissions in Guangdong Province under five scenarios. Effective predictions can be made for agricultural carbon emissions in Guangdong Province, which are expected to fluctuate between 11,142,200 tons and 11,386,000 tons in 2030. And compared with other machine learning and neural network models, the Isomap–ACO–ET model has a better prediction performance with an MSE of 0.00018 and an accuracy of 98.7%. To develop low-carbon agriculture in Guangdong Province, we should improve farming methods, reduce the intensity of agrochemical application, strengthen the development and promotion of agricultural energy-saving and emission reduction technologies and low-carbon energy sources, reduce the intensity of carbon emissions from agricultural energy consumption, optimize the agricultural planting structure, and develop green agricultural products and agro-ecological tourism according to local conditions. This will promote the development of agriculture in Guangdong Province in a green and sustainable direction.