We evaluated different lymphocyte populations and levels of plasma cytokines in peripheral blood as well as inflammatory infiltration and expressions of cytokines in lung tissues derived from macaque under long-term stimulated microgravity through being suspended in an antiorthostatic position so as to identify relevant immune parameters and to understand potential mechanisms of lung injury. Fifteen healthy male rhesus macaques were randomly divided into groups 1 (control, n = 5), groups 2 (head-down tilting for 6 weeks, n = 5), and groups 3 (head-down tilting for 6 weeks and recovery for 4 weeks, n = 5). Lymphocyte subsets in peripheral blood were analyzed using flow cytometry and the concentrations of 14 cytokines in plasma were measured with Luminex multiplexing technology. HE staining and transmission electron microscopy were employed to investigate the morphologies and subcellular structures of lung tissues. Immunohistochemistry and real-time PCR were employed to explore mRNA and protein expressions of cytokines in lung tissues. Immunohistochemical demonstrations were detected for CD3, CD4, CD8 T lymphocytes, CD20 B lymphocytes, and CD68 macrophages in lung tissues. Compared to group 1, groups 2 and 3 showed a decrease in the percentage of CD2+T cells, CD2+CD4+T helper cells, and CD2+CD8+cytotoxic T cells as well as an increase in the expression of CD95 on the surface of T lymphocytes in peripheral blood. The serum cytokine levels of IL-18 and TNF-α were increased in group 2 when compared to groups 1 and 3. HE and TEM observed changes in the structure and ultrastructure of lung tissues in groups 2 and 3. The number of CD3+T cell, CD4+T cell, CD8+T cells, and CD68+macrophage and the expression levels of IL-1β, IL-6, and IL-18 in lung tissues were increased in groups 2 when compared with groups 1 and 3. Our data suggested that long-term microgravity might alter the functions of immune system and cause lung damage, changing lymphocyte distribution and functions as well as cytokine production.