Agricultural production efficiency in Taiwan of China in 2015 is studied by using three-stage DEA model. The results show that total output value of agriculture, forestry, animal husbandry and fishery is taken as output index, while employees of agriculture, forestry, animal husbandry and fishery, number of tractors, investment in dry land and paddy field are taken as input indexes, which meets "isotropic" condition assumption of model application. Natural disaster, number of workers in agricultural production and marketing class, expenditure on farmland water conservancy are not favorable for the promotion of agricultural production efficiency, while multiple cropping index is favorable for promoting agricultural production efficiency. Three-stage DEA model effectively eliminates the influences of environmental and random factors on agricultural production efficiency. After environmental and random factors are eliminated, comprehensive technical efficiency in Taiwan of China declines because of the decline of pure technical efficiency. Each county and city of Taiwan could be divided into different types according to pure technical efficiency and scale efficiency, and it can have some emphasis in improving agricultural production efficiency according to their own efficiency characteristics.