The invention relates to a method for controlling the emission of a natural gas engine, which is characterized in that: a pulse spectrum map of engine air-fuel ratio is controlled by different regions; NOx emission in a cylinder is effectively controlled by controlling the air-fuel ratio through different regions; meanwhile, the HC and CO emission is reduced by adopting an oxidation catalyst. Theperformance development and the electrical control calibration of the engine are carried out by adopting the control method; the emission of the engine reaches Europe III Standard; meanwhile, the engine maintains the dynamic property equivalent to that of the original diesel engine and has stable combustion and low noise.