For the poor intake uniformity of constant-pressure intake manifold of natural gas engine, the 1D and 3D coupled numerical simulation was conducted to improve and optimize the intake manifold design by taking into consideration the valve timing, fuel and air mixing and airflow distribution for each cylinder comprehensively. The experimental results show that the unevenness of peak cylinder pressure between cylinders can be controlled within 1.5% by using the modified intake manifold when the power of generation sets is over 80% of the nominal power. The poor intake uniformity of each cylinder and great difference between exhaust temperatures are solved well through the modifications, which provides the basis for further improvement of power.