Microneedles have emerged as the new class of local drug delivery system that has broad potential for development. Considering that the microneedles can penetrate tissue barriers quickly, and provide localized and targeted drug delivery, their applications have gradually expanded to non-transdermal drug delivery recently, which are capable of providing rapid and effective treatment for injuries and diseases of organs or tissues. However, a literature search revealed that there is a lack of summaries of the latest developments in non-transdermal drug delivery research by using biomedical polymeric microneedles. The review first described the materials and fabrication methods for the polymeric microneedles, and then reviewed a representative application of microneedles for non-transdermal drug delivery, with the primary focus being on treating and repairing the tissues or organs such as oral cavity, ocular tissues, blood vessels and heart. At the end of the article, the opportunities and challenges associated with microneedles for non-transdermal drug delivery were discussed, along with its future development, in order to provide reference for researchers in the relevant field.