Microlenses have wide applications for light beam focusing or shaping in micro-optical systems. However, it remains challenging for conventional microfabrication methods to rapidly fabricate arrays of microlenses with complex profiles like lens-on-lens structures. In this paper, we present the rapid fabrication of polymer microlenses with lens-on-lens structures by using a digital optical μ-printing technology. An improved dynamic optical exposure method is developed to directly and precisely fabricate polymer top-lensed microlenses (TLMLs). Arrays of TLMLs with either elongated focal depth or two separate foci have been numerically investigated and experimentally demonstrated.