To explore the relationship between plant secondary compounds and the immune functions of small mammal herbivores, this study measured the effects of plant quercetin on immune organ development and concentrations of several key cytokines of Microtus fortis fed diets containing 0, 1.5%, 3%, 5%, or 8% quercetin. The results showed that the indices of the spleen and the thymus of M. fortis fed 5% quercetin were increased by 14.48% (P < 0.05) and 11.67% (P < 0.05), respectively, and IL-2 and IL-10 were increased by 8.9% (P < 0.05) and 14.99% (P < 0.05), respectively; TNF-α and IL-1β were decreased by 11.13% (P < 0.05) and 17.40% (P < 0.05), respectively, when compared those of the control. When quercetin concentration reached 8%, the indexes of the spleen and the thymus were decreased, IL-2, and IL-10 secretions were suppressed, while TNF-α and IL-1β levels were increased. Dietary plant quercetin affected the immune organ development and cytokine secretion of M. fortis in a dose-dependent manner.