This paper discusses the problem of design and optimization of low-energy transfer orbit with multi-body environment. A new integrative method is proposed to effectively solve the problem, in which the parameterized patched manifolds in CR3BP(circular restricted three-body problems), the shape-based method with multi-body environment, the homotopic method with multi-body environment, and the low-thrust capturing and descending algorithm with multi-body environment are all included. Firstly, the parameters describing the patched manifolds in CR3 BP are optimized until the least total absolute velocity increment has been got, including the employment of the shape-based method with multi-body environment. Secondly, the low-thrust control laws of the transfer orbit are optimized employing the homotopic method with multi-body environment that transfers the fuel optimization problem to an easier energy optimization problem. Thirdly, the low-thrust descending orbit around Mars is computed using the laws proposed in this paper. As a typical example, the Earth-Mars transfer orbit design is discussed. The results showed that the parameters describing the patched manifolds could be optimized by the DE(differential evolution) algorithm effectively; the homotopic method with multi-body environment could get the optimal value that meets the first order optimality conditions; and the low-thrust descending orbit could effectively be captured by Mars and finally become a circular parking orbit around it by the hypothesis control laws proposed in this paper. It shows that the final fuel cost is much less than the optimal transfer in the patched two-body problems. In conclusion, the method proposed in this paper could effectively solve the low-energy low-thrust optimal control problem in multi-body environment for the future deep space explorations. This paper discusses the problem of design and optimization of low-energy transfer orbit with multi-body environment. A new integrative method is proposed to effectively solve the problem, in which the parameterized patched manifolds in CR3BP (circular restricted three-body problems) the shape-based method with multi-body environment, the homotopic method with multi-body environment, and the low-thrust capturing and descending algorithm with multi-body environment are all included. optimized until the least total absolute velocity increment has been been got, including the employment-the shape-based method with multi-body environment. Secondary, the low-thrust control laws of the transfer orbit are optimized employing the homotopic method with multi-body environment that transfers the fuel optimization problem to a easier energy optimization problem. Thirdly, the low-thrust descending orbit around Mars is computed usi ng the laws proposed in this paper. As a typical example, the Earth-Mars transfer orbit design is discussed. The results showed that the parameters describing the patched manifolds could be optimized by the differential motion (DE) algorithm; the homotopic method with multi-body environment could get the optimal value that meets the first order optimality conditions; and the low-thrust descending orbit could effectively be captured by Mars and finally became a circular parking orbit around it by the hypothesis control laws proposed in this paper. It shows that the final fuel cost is much less than the optimal-transfer in the patched two-body problems. future deep space explorations.