Procedures for cytomic screening were developed for identifying compounds with immuno-modulating properties from the crude extracts of natural products. Human peripheral blood mononuclear cells (hPB-MNCs) were first cultured with different natural crude extracts for 12 hours in culture media. By analyzing the expression of early activation CD69 marker, the potential immuno-activating properties of ethanol extracts of Calocedrus formosana were observed. By the double staining of antibodies recognizing CD69 and specific cell type markers, the increase of CD69 expressions was observed in CD3 and CD14 cell populations. To examine the immuno-activating properties in CD3 T cells and CD14 monocytes, the extracts were further purified. From NMR and mass spectra, sugiol was identified as a pure functional compound, and its immuno-enhancing activities were confirmed by CD69 expressions in the affected cell populations. Furthermore, to clarify the sugiol-affected subpopulations in CD3 T cells, CD3 T cell activation in association with increase in CD8 cytotoxic T cells subpopulation was observed. To address the effect of sugiol on each isolated cell population, we found that the expression of CD69, CD80, and CD86 increased in CD14 monocytes upon exposure to sugiol, whereas for CD3 T cells, sugiol failed to induce the expressions of CD69 and CD25. However, T cell activation by coculturing monocytes and T cells suggests that the sugiol activation of T cells in hPB-MNCs involved the accessory mechanisms of sugiol-primed monocytes. Therefore, cytomic screening as a multiple-parameter screening strategy reveals the plasticity for immuno-functional studies, leading to the applications to discover new drugs of specific immunomodulating activities.