Maneuvering to a free return trajectory is a vital abort means for crewed lunar missions. A novel method of solving the fuel optimization of free return abort trajectory for Earth-Moon transfer by two-stage transformation on optimization model and Bayesian optimization is documented. Two new design variables—perilune altitude and transfer time from earth to perilune, instead of the original injection velocity vector, are introduced to transform the general model into a two-dimensional model. Each feasible abort trajectory is determined by a numerical method including initial estimate and exact solution. Then the characteristics of the relationship between the new variables and the fuel objective of impulse maneuver are applied to further transform the model into a one-dimensional model. Based on the Bayesian optimization method, fuel optimization is successfully and efficiently implemented for the free return abort trajectory at multiple abort moments during the Earth-Moon transfer. Furthermore, the influence of the initial Earth-Moon phase on the result of fuel optimization is presented. Numerical simulations are conducted to demonstrate the efficacy of the proposed method.