The effects of rice-crayfish integrated mode on the soil microbial community functional diversity and soil fertility in waterlogged paddy field were investigated. The results indicated that the average well color development values (AWCD) of rice-crayfish integrated mode were higher than these of semi-late rice monoculture mode in 0–50 cm soil layer, and soil AWCD values of the former mode were significant greater than these of the letter mode in 25–50 cm soil layer. Compared with the semi-late rice monoculture mode, the rice-crayfish integrated mode significantly increased McIntosh index and utilization of amines and acids by soil microorganisms in 0–25 cm soil layer, and the mode also significantly increased Shannon index, McIntosh index and utilization of sugars, alcohols and acids by soil microorganisms in 25–50 cm soil layer. The principal component analysis suggested that the differentiations of soil microbial communities were mainly caused by sugars and acids. Soil carbon and total nitrogen of the rice-crayfish integrated mode were significantly lower than these of the semi-late rice monoculture mode in 25–50 cm soil layer, and the soil carbon and total nitrogen were decreased by 41.8% and 34.8%, respectively, in the rice-crayfish integrated mode compared with the semi-late rice monoculture mode. But there were no significant differences in soil nutrients between the two culture modes in 0–25 cm soil layer. Therefore, the rice-crayfish integrated mode increased the activity and functional diversity of soil microbial community, especially for sub soil, while decreased the contents of soil carbon and total nitrogen in sub soil.