Fresnel lens arrays are widely employed in concentrator photovoltaics, photonic devices, and integral imaging systems. In this study, a rapid non-isothermal imprinting process for Fresnel lens arrays was proposed. In this process, a heated mold with microstructures was momentarily pressed onto a thermoplastic polymer surface that was initially kept at room temperature. The microstructures of the mold can be copied completely to the polymer substrate by imprinting consecutively until a continuous surface Fresnel lens array is obtained. Different from more traditional molding processes, the substrate does not need to be heated and cooled repeatedly in the replicating process. In addition, the imprinting process is carried out at room temperature, which can greatly reduce the thermal cycle time and energy consumption. Generally speaking, the material flow and stress distribution of the substrate need to be monitored so that the microlenses with a high precision surface finish can be produced in the non-isothermal imprinting process. To verify this, the finite element method (FEM) model for the non-isothermal process was established, and the feasibility of this process was analyzed. A hexagonal continuous surface Fresnel lens array was then fabricated, and its geometrical contour and imaging performance were tested. The experimental results showed this new process could be an effective and low-cost optical fabrication technology for high-quality production of Fresnel lens arrays.