The yak is an agricultural animal with strong disease resistance in Qinghai–Tibet Plateau. Immune organs are directly involved in the body’s immune response and protect it from external aggression. In this study, we characterized and evaluated the main markers of interleukin (IL)-1β, IL-17a, hypoxia inducer factor-1 (HIF-1)α, and heat shock protein 90 (HSP90) in the lymph nodes, spleen, thymus, and hemal nodes of adult yaks using network informatics, molecular cloning, immunohistochemistry, real-time quantitative polymerase chain reaction (RT-qPCR), and western blotting. We first cloned the IL-1β and IL-17a mRNA of yaks. A significant feature was the higher IL-1β and IL-17a expression in the lymph nodes than in the spleen, hemal nodes, and thymus. Immunohistochemistry and immunofluorescence revealed that IL-1β and IL-17a cells were mainly located in the paracortex area of the lymph nodes and the T-cell-dependent area in the hemal nodes and spleen. Several HIF-1α proteins were detected in the cortex of the hemal nodes mantle, while HSP90 was detected in the lymphoid nodules of the hemal nodes and lymph nodes. This study sheds light on the relationship between the morphology and function of these organs and provides an important reference for studies on the participation of yak immune organs in immune responses.