In recent years, check dams on the Loess Plateau have played an important role in mitigating soil erosion and silting land for land reclamation. But compared with earth and rock dams, the flood control standard of check dams is not high, and the dam break is more likely to occur. Check dams are distributed in a number of small basins in the form of stairs, forming a complex dam system network, which brings great challenges for the correct evaluation of the risk of failure. This paper adopted a failure risk analysis model of check dam systems based on hydrological calculations in small watersheds and considered the complex inflow conditions and the corresponding calculation program FT-IWHR. Taking the check dam reinforcement project in the Xi'ao watershed in Shanxi Province as an example, under the checking conditions (the flood return period is 200 years), the current check dam system was analyzed for continuous collapse risk. At the same time, the feasibility analysis of the danger-removing and reinforcement scheme was carried out under the two working conditions of the current check dam system and the siltation surface of each dam reaching the design siltation elevation after a few years. The results showed that the current 8# medium dam did not meet the flood control standards, and the critical rainfall was only 133 mm. The critical rainfall would increase to 945 mm after adding the spillway of 6 m wide and 3 m high, and the critical rainfall would decrease to 886 mm after the siltation surface reached the siltation elevation. both of which could meet the flood control requirements. And the addition of a spillway could effectively reduce the risk caused by the rise of the siltation surface. The risk analysis method and practical application results of check dam system have certain reference value for flood control risk analysis and planning design of check dam system under extreme rainfall.