Abstract: The integrated rice-crayfish system is an emerging complex ecological system of planting and breeding in the middle and lower reaches of the Yangtze River in China. The study of N and P cycling characteristics and the profit and loss status of N and P in the integrated rice-crayfish system is of great significance to rationally regulate the nutrient cycling and balancing of the integrated rice-crayfish system and guide the optimal management of the N and P. In this study, a field experiment was conducted to study the cycling characteristics and apparent balance of N and P under the integrated rice-crayfish system using an input-output method, with the rice monoculture system as the control. The results showed that the output/input ratios of N and P in the crayfish subsystem were 0.62 and 0.44, respectively. Inside the crayfish subsystem, the N and P were the largest in the feed input, accounting for 92.9% and 96.4% of the total input, respectively; the output of adult crayfish N and P was the largest, accounting for 53.3% and 59.5% of the total output, respectively. Under the current input levels, the apparent balance of both N and P in the soil subsystems of the two systems were in surplus, and the surplus of N in the soil subsystem of the integrated rice-crayfish system was higher than that of the rice monoculture system, while the surplus of P was lower than that of the rice monoculture system. The N and P output/input ratios of the integrated rice-crayfish system and the rice monoculture system were both less than 1, and the N and P output/input ratio of the integrated rice-crayfish system were less than that of the rice monoculture system. The integrated rice-crayfish system increased the amount of N and P in sequestered soil, and the N and P levels in sequestered soil of the integrated rice-crayfish system were higher than those of the rice monoculture system by 49.2 kg·hm^-2 and 9.1 kg·hm^-2, respectively. The integrated rice-crayfish system increased the apparent loss of N and P in the system, and the apparent losses of N and P of the integrated rice-crayfish system were higher than those of the rice monoculture system by 10.2 kg·hm^-2 and 1.0 kg·hm^-2, respectively. It can be seen that the integrated rice-crayfish system reduces the output/input ratio of N and P and promotes the accumulation of N and P in the soil but increases the apparent loss of N and P in the system.