Transmission gear whine noise is one of the main noise problems in powertrain NVH, which is caused by dynamic meshing force of gear pairs, it acts as transmission error. Due to the coupling effects of transmission gears, shaft, bearings and housing, it needs comprehensive management from many aspects to solve the problem of gear whine noise. Aiming at gear whine noise of a 4-speed AMT used in electric bus, the main noise sources is identified by using the order tracking analysis approach firstly. Secondly, gear misalignment and contributions of system deformation to the misalignment is analyzed by means of simulation tools, and the factor is taken into account in the subsequent gear modification design. At last, based on the improved Smith slice method, the calculation model of transmission error of helical gears is established. Combining with the various driving conditions of vehicle, using reducing peak to peak value of transmission error, Uniform distribution of tooth surface load and other indicators as a mean to reduce the impact of vibrations and noise, an improved particle swarm optimization (PSO) algorithm is adopted to optimize modification parameters to obtain the best micro-modification tooth surface. The optimization results show that this optimization method proposed in this paper can effectively eliminate gears whine noise of transmission.