Cadmium (Cd) and high dietary intake of molybdenum (Mo) can cause multiple-organ injury in animals, but the co-induced toxicity of Mo and Cd to spleen in ducks is not well understood. The aim of this study was to investigate the co-induced effects of Mo and Cd on the mRNA expression levels of inflammatory cytokines and heat shock proteins (HSPs) in duck spleens. Two hundred forty healthy 11-day-old ducks were randomly divided into six groups and treated with a commercial diet containing Mo or/and Cd. After being treated with Mo or/and Cd for 30, 60, 90, and 120 days, the mRNA expression levels of nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX-2), HSP60, HSP70, and HSP90 were examined in duck spleens. Histopathology was examined in duck spleens at 120 days. The results indicated that the mRNA expression levels of HSPs were significantly upregulated in the co-induced groups (P < 0.01), while these decreased in the high dietary intake of Mo combined with Cd group at 120 days. Exposure to Mo or/and Cd upregulated the mRNA expression levels of NF-κB, COX-2, and TNF-α in the combination groups (P < 0.01). Furthermore, severe congestion, bleeding, splenic corpuscle structure fuzzy, wall thickness of sheath artery thickening, and oxyhematin were observed in the spleens of combination groups. Meanwhile, the organizational structure damage of the combined groups was more severe than that of the other groups. These results suggested that exposure to Mo or/and Cd might lead to tissue damage, and high expression of HSPs and inflammatory cytokines may play a role in the resistance of spleen toxicity induced by Mo or/and Cd. Interaction of Mo and Cd may have a synergistic effect on spleen toxicity.