The lens arrays are widely used in advanced industrial fields such as national defense, medical care, and aerospace due to its special optical performance. Single-point diamond turning based on fast/slow tool servo technology is an important machining method to fabricate lens arrays. However, the constant-angle or constant-arc-length sampling of the spiral tool trajectory leads to the uneven distribution of surface data point cloud, which makes the theoretical morphology of microstructure deviate from their machined morphology, and seriously restricts the high precision, high flexibility and large-scale fabrication of the microstructure. This research provided a novel fabrication method for machining multi-boundary lens arrays by employing tool offset end-fly-cutting method which interchanged the position of the tool and workpiece, and a mathematical model was established to generate the uniform tool trajectory covering the multi-boundary lens array. Through the comparison of measured and simulated results, the root-mean-square (RMS) error of multi-boundary lens array's sectional curve is below 1 μm, proving the effectiveness of the machining method. This method provided a new technical scheme for the fabrication of multi-boundary lens arrays, and provided a theoretical reference for machining multi-scale microstructures.