Based on methods such as stochastic frontier production function, this paper analyses the changes of single factor productivity (SFP) and total factor productivity (TFP) of agriculture in the five Central Asian countries, during the period of 1992 to 2017. The research results show that the agricultural output in most of the five Central Asian countries has increased steadily, while agricultural labor productivity has shown a growth trend. With the exception of Kazakhstan, the land productivity of the other four countries shows a growth trend. In terms of factor input, the number of agricultural workers in the five Central Asian countries mainly shows a trend of decrease, with the input of chemical fertilizer increasing, and the amount of agricultural machinery increasing or decreasing within a small range. The total factor productivity in the five Central Asian countries has improved, but it is still at a low level. The policy suggestions contained in the research conclusions are as follows: (1) Promote the growth of agricultural TFP in the five Central Asian countries, and strengthen the emphasis on the input and allocation of agricultural factors; (2) be aware of the innovation of agricultural technology, as well as the promotion and diffusion of existing agricultural technologies, and improve the overall technical efficiency of agriculture; and (3) accelerate the effective flow of capital and other elements to the agricultural sector, improve infrastructure, better release the “dividend” of science and technology, and enhance the output efficiency.