Sexual transmission has become the major route of acquiring human immunodeficiency virus type 1 (HIV-1) globally. Understanding the mechanism of HIV-1 mucosal infection will be helpful for development of new effective strategies to block HIV-1 mucosal transmission. Currently, study of the mechanism of HIV-1 mucosal infection majorly depends on in vitro cell culture systems and non-human primate animal models. Recently, a novel tissue explant model (including human vaginal-genital and colorectal tissue) was established, which could elucidate the biological process of HIV-1 mucosal infection from crossing over the membrane to reaching the basal. Therefore, the model can be applied to the study of mechanism, as well as the safety and efficacy evaluation in pre-clinical study of biomedical prevention strategies. In this review, we summarized the recent progress about human mucosal explants model including the sources of tissues, technical characteristics and their application to study the mechanism of HIV-1 sexual transmission and evaluation of prevention strategies. Based on our recent study results, we also provided our opinions about development of novel explant models and their application.