Aiming at the energy dissipation problem of the single open ditch of the ship lock bottom long-culvert，we combine with the Shanxiu second lock in Zuojiang River in Guangxi province，establish the three-dimensional turbulent mathematical model of the filling and emptying system with side branch hole in the ship lock bottom long-culvert，carry out the three-dimensional simulation for the filling operation period of the chamber，and compare and analyze the internal flow field distribution，velocity distribution uniformity，residual specific flow energy and other parameters of the original design scheme and three optimization schemes. The results show that the energy dissipation performance of the system is significantly enhanced by laying a longitudinal sill for the open ditch. The values of the corresponding flow velocity distribution and specific residual flow energy of the optimization schemes increase slightly beyond a critical value （1.2 m） of the height. The results can indicate that the space for enhancing energy dissipation is limited after the height reaches 1.2 m.