The operational planning of ventilation system of urban complex extralong tunnel is difficult due to its complex calculation. Hence, the ventilation volume of north line tunnel and south line tunnel under different operating conditions of an urban complex extralong tunnel is simulated and calculated by ventilation software SES to verify the reliability of initial ideal operation design. And then the total installed power of tunnel fan and discharge ratio of tunnel outlet under different vehicle speed conditions are calculated and put into comparison to determine the opening positions and quantity of tunnel axial fan and jet fan. Finally, the concentrations of pollutants inside and outside the tunnel are analyzed to verify the feasibility of the optimized scheme. The results show that: (1) The piston wind generated by traffic cannot meet the needs of air volume for the normal operation of the complex tunnels, and some jet fans need to be turned on. (2) The drainage effect of shafts close to the main entrance/exit of the tunnel is poor, and the ventilation energy consumption of the tunnel will be increased after opening the shafts.