Objective: To study the immunosuppression effect on the thymus of muscovy ducks after infected with muscovy duck reovirus (MDRV) and H9 influenza virus (AIV)., Methods: After 8-day-old birds were infected with MDRV or H9 AIV, or both, the morbidity and mortality were totaled, the morphology and ultra-structure of the thymus were observed, proliferation ability of thymus cell were detected and the virus distrubition were detected by RT-PCR., Results: After H9 AIV infection, The morbidity was low (10%) and without death. No obvious pathological change was observed on the thymus, whereas the proliferation ability of thymus cell was obviously suppressed. After MDRV infection, The birds grew slow, the morbidity was 80% and mortality was 50%. Thymus was atrophy appearing local necrosis and proliferation ability of thymus cell was obviously suppressed. After co-infection with MDRV and H9 AIV, the birds grew even slower growth. The morbidity was 90% and mortality was 70%. The thymus was atrophy appearing the lymphopenia and local necrosis and proliferation ability of thymus cell was also more obviously suppressed than MDRV infection. Virus duration time and detection ratio in co-infection group were more than in AIV and MDRV group., Conclusion: H9 AIV could lead to minor immunosuppression and MDRV could cause serious immuno-suppression. H9 AIV could aggravate the immunosuppression of thymus after co-infected with MDRV, so MDRV and H9 AIV infection had synergic effect on immunosuppression of the thymus.