We retrospectively examined 33,142 persons living with HIV (PLWH) in Taiwan from a nationwide database to assess sex-stratified trends and risk of all-cause mortality under different transmission categories from 1984 to 2016. Overall, 61.25% were men who have sex with men (MSM), 14.37% were men who have sex with women (MSW), 18.32% were male persons who inject drugs (M-PWID), 3.30% were women who have sex with men (WSM), and 2.74% were female PWID (F-PWID). All-cause mortality (per 100 person-years) among heterosexual people and PWID was higher in men (4.04 and 3.39, respectively) than in women (2.93 and 2.18, respectively). In each sex-stratified transmission category, the all-cause mortality reduced substantially from 1984-1996 to 2012-2016, but evolved distinctly from 2007-2011 to 2012-2016. Since 2007-2011, the decline in all-cause mortality has slowed notably in the groups with sexually transmitted HIV, but has increased in PWID, surpassing even that among groups with sexually transmitted HIV in 2012-2016. PLWH with sexually transmitted HIV had lower risks of all-cause mortality than PWID, regardless of sex. Sex and transmission category did not interact significantly on all-cause mortality. Understanding the reasons for the distinct evolving trends of all-cause mortality in each transmission category serves as a reference for developing strategies to reduce mortality in PLWH in Taiwan further.