Multiple softwares were required in the traditional design process of LED free-form surface lens. It is obvious that this process is complicated and inefficient. Moreover, when the model was transferred from 3D modeling software to optical simulation software, the file format had to be changed to solve the problem of the software compatibility. Note that some subtle changes were inevitably introduced to the model by such an operation, such as the generation of cracks or tiny deformation which would seriously affect the light efficiency and the degree of illumination uniformity. A new design method was presented in this paper which was used to directly generate model in the optical simulation software by using Scheme language. In this paper, the method of mesh division was applied to design the LED free-form surface lens with rectangular lighting. After the corresponding surface configuration was obtained, 3D modeling software and the Scheme language programming were used to generate lens model respectively. With the help of optical simulation software, a light source with the size of 1 mm in diameter was used in experiment, in which total one million rays were computed. The simulated results could be acquired by both models. It can be seen that the model deformation problems caused by the process of the model transfer could be prevented by using Scheme language, and the degree of illumination uniformity was also increased from 67% to 93.5%. Meanwhile, only 5 seconds were needed in modeling process by Scheme language which was more efficient than 3D modeling software.