According to the panel data of 21 prefecture-level cities in Guangdong Province from 2010 to 2016, the input-output index of agricultural production efficiency has thus been constructed, with the three-stage DEA model adopted to empirically analyze the agricultural production efficiency of Guangdong Province. The results show that the agricultural comprehensive technical efficiency of Guangdong province has kept improving, with the scale efficiency being the main reason that restricts the agricultural production efficiency in most areas; the urbanization level, science and technology and education level all exert a positive effect on the agricultural production efficiency, while the affected area has a negative effect on the agricultural production efficiency, the agricultural financial expenditure fails to achieve the ideal effect on the agricultural production efficiency. There is a distinct discrepancy between the agricultural production efficiency of the Pearl River Delta and the northern part of Guangdong Province, with the former being the highest area and the latter the lowest one of the production efficiency. A proposal has thus been madeof the improvement of the production efficiency of each research unit, with a view to promoting the process of new urbanization, cultivating new type of professional farmers, guiding the development of green cycle, high quality and high efficiency characteristic agriculture, and perfecting the land circulation system.