There are still significant challenges in the accurate and uniform manufacturing of microlens arrays (MLAs) with advanced ultra-precision diamond cutting technologies due to increasingly stringent requirements and shape complexity. In this paper, an optimum machining process chain is proposed based on the integration of a micro-abrasive fluid jet polishing (MAFJP) process to improve the machining quality by single point diamond turning (SPDT). The MLAs were first machined and compensated by SPDT until the maximum possible surface quality was obtained. The MAFJP was used to correct the surface form error and reduce the nonuniformity for each lens. The polishing characterization was analyzed based on the computational fluid dynamics (CFD) method to enhance the polishing efficiency. To better polish the freeform surface, two-step tool path generation using a regional adaptive path and a raster and cross path was employed. Moreover, the compensation error map was also investigated by revealing the relationship between the material removal mechanism and the surface curvature and polishing parameters. A series of experiments were conducted to prove the reliability and capability of the proposed method. The results indicate that the two integrated machining processes are capable of improving the surface form accuracy with a decrease in PV value from 1.67 µm to 0.56 µm and also elimination of the nonuniform surface error for the lenses.