Objective Based on time-coupled multiscale coupling algorithm, to simulate the hemodynamics after systemic-pulmonary shunt procedure on single ventricular patient so as to obtain the local three-dimensional (3D) fluid field and global hemodynamic information before and after surgery. MethodsFirstly, the 0D-3D coupled multiscale hemodynamic model of systemic-pulmonary shunt procedure was established based on the lumped parameter model (0D) before surgery and the shunt model (3D), then the 0D-3D interface coupling condition and the time coupling algorithm were discussed. Secondly, the multiscale simulation of 3D CFD (computational fluid dynamics) model coupled with 0D lumped parameter model was realized based on lattice Boltzmann method. Finally, the multiscale simulation results were compared with patient’s 0D simulation results to study the hemodynamic changes before and after surgery. Results The global hemodynamic change and local 3D flow pattern were obtained by this multiscale simulation. The pulmonary blood flow distribution ratio was increased from 32.21% to 57.8%. Conclusions The systemic-pulmonary shunt procedure can effectively increase the blood supply of pulmonary circulation by implanting the shunt between the systematic circulation and pulmonary circulation. The geometrical multiscale method can effectively simulate both the coarse global and detailed local cardiovascular hemodynamic changes, which is of great significance in pre-operation planning of cardiovascular surgery.