Background The affecting factors of mucocutaneous manifestations in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients remain unclear in China. Methods A retrospective analysis was conducted among HIV/AIDS patients in Yunnan, China. The demographic data, mucocutaneous manifestations, CD4 cell counts, and antiretroviral therapy (ART) regimens were collected. The effects of CD4 cell count and ART on the spectrum of mucocutaneous manifestations were evaluated. Results Among 508 HIV/AIDS patients, 86.0% of cases showed mucocutaneous manifestations. The average CD4 cell count (176 cells/mu l) of the patients with manifestations was significantly lower than those without manifestations (328 cells/mu l) (P < 0.001). Diseases such as herpes zoster, oral candidiasis, condyloma acuminatum, genital herpes, oral leukoplakia, talaromycosis, cryptococcosis, and HIV-PPE (pruritic papular eruption) were represented quite frequently in patients with CD4 cell count <200 cells/mu l (P < 0.05), but eczema was suffered by those with CD4 cell count >= 200 cells/mu l (P < 0.05). ART could decline the incidence of herpes zoster, oral candidiasis, condyloma acuminatum, genital herpes, oral leukoplakia, talaromycosis, and cryptococcosis (P < 0.05). Conclusions Mucocutaneous manifestations are closely related to the CD4 cell count and can be used as early predictors of HIV/AIDS and immune status in clinic. ART could reduce the incidence of certain mucocutaneous manifestations.