Objective We examined the expression level of plasma cytokines in SIVmac239-infected rhesus monkeys before and during antiviral treatment and assessed correlations with disease characteristics. Methods The SIVmac239 virus was administered intravenously to healthy Chinese rhesus monkeys, which were then treated with HAART (Highly active antiretroviral therapy) as an AIDS treatment model. Flow cytometry was used to detect CD4⁺T cell counts in peripheral blood, and Luminex was used to detect plasma cytokines. Results After HAART treatment, the plasma viral load of SIVmac239-infected rhesus monkeys decreased below the detection limit, and the CD4⁺ T cell count and CD4⁺ / CD8⁺ ratio recovered to pre-infection levels. Expression of all cytokines detected after infection, except IL-8, was elevated. After HAART treatment, except for a decrease in IP-10 expression levels, IL-8 remained unchanged and other cytokine levels continued to rise. After stopping drug treatment, levels of pro-inflammatory factors TNF-α, antiviral factors IFN-γ and IFN-α, and the expression of chemokine MCP-1 decreased. The pro-inflammatory factor IL-6 and the anti-inflammatory factor TGF-siowere most strongly correlated with plasma viral load. Conclusions Most cytokines were elevated after infection and HAART treatment, and expression of most cytokines decreased after stopping the drug, although they remained higher than normal. Levels of IL-6, TGF-β1, and IP-10 cytokines are consistent with clinical manifestations regardless of changing trends or correlations with disease characteristics.