Human γδ T cells are typically divided into Vγ9Vδ2 and non-Vγ9Vδ2 cells, but their detailed heterogeneity remains to be fully elucidated, especially in the liver where they are enriched. Here we analyze liver sinusoidal γδ T cells from healthy donors, with or without latent human cytomegalovirus (HCMV) infection, by performing single-cell RNA sequencing with antibody-derived tags. Vγ9Vδ2 cells are characterized by PLZF expression, and classified into type 1 and type 3 immunity-associated clusters. In contrast, non-Vγ9Vδ2 cells are characterized by Helios expression, and their clusters display naïve-to-effector differentiation processes, which are accelerated by HCMV infection. Notably, among non-Vγ9Vδ2 cells, we identify a novel liver-resident CD56hiCD161− cell population with a distinct TCR repertoire, which is markedly enriched in HCMV-seropositive donors. These cells exhibit IL-15-induced NK-like cytotoxicity, but limited responsiveness to TCR stimulation. Our findings reveal liver sinusoidal γδ T cells’ heterogeneity in the context of latent HCMV infection, and their functions.