We present a rapid and highly efficient method to form microstructure of poly(ethylene glycol) (PEG)-based acrylates by microwave-induced thermal crosslinking. PEG-based polymeric microstructures such as polymer microarrays and microwells were fabricated on 3-(trimethoxysilyl)propyl methacrylate (TMSPMA)-coated glass slides that were placed on top of a silicon wafer. In comparison to ultraviolet (UV) irradiation curing, microwave-induced thermal crosslinking could be completed within 10 s, without thermal degradation or oxygen inhibition in the presence of ambient oxygen. Furthermore, the activation of surviving free radical impurities by microwave-induced heating enabled crosslinking even without an exogenous radical initiator (e.g., 2,2'-azoisobutyronitrile (AIBN)). This approach can be beneficial for fabricating various PEG-based microstructures for high-throughput screening assays, cell-based biosensors, and biomedical microdevices.