Microneedles (MNs) as a novel transdermal drug delivery system have shown great potential for therapeutic and disease diagnosis applications by continually providing minimally invasive, portable, cost-effective, high bioavailability, and easy-to-use tools compared to traditional parenteral administrations. However, microneedle transdermal drug delivery is still in its infancy. Many research studies need further in-depth exploration, such as safety, structural characteristics, and drug loading performance evaluation. Finite element analysis (FEA) uses mathematical approximations to simulate real physical systems (geometry and load conditions). It can simplify complex engineering problems to guide the precise preparation and potential industrialization of microneedles, which has attracted extensive attention. This article introduces FEA research for microneedle transdermal drug delivery systems, focusing on microneedle design strategy, skin mechanics models, skin permeability, and the FEA research on drug delivery by MNs.