Floods cause environmental hazards and influence on socio-economic activities. In this study, we evaluated the historic flood frequency at a confluence in the middle Yellow River, China. A non-parametric, multivariate, empirical, orthogonal function matrix model, which consists of time correlation coefficients of flood discharge at different gauge stations and flood events was used for the analysis of flood frequency. The model addresses the characteristics of confluent floods such as frequency and the probability in multiple tributary rivers. Flood frequency analysis is often coupled with studies of hydrological routing processes that reduce the flood capacity of the rivers. Flood routing to the confluence were simulated using kinematic wave theory. Results of this flood frequency analysis showed that flooding frequency has intensified in the past 500 years, especially during the 19th century. Flooding in streams above the confluence was more frequent than in streams below the confluence. Over the last 2000 years, concurrent flooding in multiple tributary rivers accounted for 67.5% of the total flooding in the middle Yellow River. Simulation of flood routing processes shows that the decreased flooding capacity and elevated river bed of the shrunken main channel leads to an increased flood wave propagation time (24-52.3 h) in the study area after 1995. The model indicates that human activities, such as constructions of the Sanmenxia Dam, have changed flood routing boundary conditions and have contributed to the increased flood frequency at the confluence.