A trimming method to optimize the configuration of a three-dimensional asymmetric nozzle with shape transition, which aims to obtain good aerodynamic performance and to save weight at the same time, is presented in this paper. Then the effects of the entry shape on the performance of the three-dimensional nozzle are investigated. The streamline tracing involved in an axisymmetric flowfield with optimal thrust is employed to obtain the inviscid contour of the three-dimensional nozzle with shape transition, and the reference temperature method is applied to correct the thickness of the boundary layer. The performance of the designed nozzle is obtained by using computational fluid dynamics. The calculated results show that the trimmed nozzle gains increases in the lift and pitching moment by 427.00% and 10.80%, respectively, with only a 0.76% decrease in the axial thrust coefficient, while the weight can be reduced by as much as 37.51%. For the nozzles with elliptical entrances, as the axial ratio ranges from 1.0 to 2.0, the axial thrust coefficient is increased by 5.38%, while the lift is decreased by 67.74%. When considering the nozzles with rectangular entrances, as the aspect ratio ranges 1.0 to 2.0, the axial thrust coefficient is increased by 3.58%, while the lift and pitching moment are decreased by 82.09% and 16.43%, respectively. Most of the axial thrust is produced on the upper-wall and side-walls in all nozzles, and the contribution of the expansion flow along the side-walls on the thrust generation is pronounced in the nozzle with a relatively smaller entry ratio. However, the majority of the lift and pitching moment are generated on the upper-wall and lower-wall. Besides, the viscosity loss and weight can be reduced by applying the elliptical cross-section in the propulsion system.