Lens arrays are widely used in advanced industrial fields, such as national defense, medical care, and aerospace, because of their exceptional optical performance. Single-point diamond turning based on fast/slow tool servo technology is a common machining method for fabricating lens arrays; however, the constant-angle or constant-arc-length sampling of its spiral tool trajectory leads to an uneven cutting speed, and thus, the machined morphology of the lens arrays deviates from their theoretical morphology. This shortcoming seriously restricts the high-efficiency production of large-scale lens arrays, as well as reduces design accuracy. Accordingly, a novel method is proposed herein for the fabrication of multi-boundary lens arrays by tool offset end-fly-cutting. First, a mathematical model was established to generate a uniform tool trajectory for the subsequent fabrication of square and hexagonal boundary lens arrays. From a comparison of the measured and simulated results, the root-mean-square error of the sectional curves of the multi-boundary lens array is below 1 μm, proving the effectiveness of the production method. The developed method provides a new technical scheme for the fabrication of multi-boundary lens arrays and a theoretical reference for machining multiscale microstructures.