The Copula function parameters were estimated by the measured flood peak flow, and the joint probability distribution model was established to calculate the flood encounters probability of the Lianjin River and Jin River. First, four kinds of the most common Copula functions were established, and the fitting effect was evaluated by Q-Q graph and goodness evaluation criterion, and the Frank function with the best effect was selected for flood encounter analysis. The results showed that the probability of flooding in the same magnitude of Jin River and Lianjin River is relatively small. The probability of a flood in the Jin River and Lianjin River at the same time is less than 0.61%. The probability of a once every 10 years flood in the Jin River and once every 20 years flood in Lianjin River was as high as 23.01%. Finally, the MIKE11 model was used to calculate the flood surface line of Jin River and Lianjin River under this condition. The study of the flood encounter probability and the calculation result of the water surface line are of great significance to the flood control project of the city.