In order to elucidate the effect mechanism of stand characteristics on seed germination and natural regeneration of Rhododendron protistum var. giganteum, we investigated the effect of fresh and litter leaf, forest litter and forest moss aqueous extracts on its seed germination percentage and germination index. We also discussed the autotoxicity and litter allelopathy effects on the species natural regeneration. The results indicated that: (1) both fresh and litter leaf aqueous extracts inhibited seed germination, the inhibiting effect of litter leaf aqueous extracts is relatively lower than that of fresh leaf. Seed germination percentage and germination index dramatically decreased with increasing fresh leaf aqueous extracts concentrations. When the fresh leaf aqueous extracts concentration reached 10%, seed germination percentage decreased to only 8%. Thus, the species has obvious autotoxicity effect on its germination. (2) Forest litters collected under the plant canopy with different distance (0, 2, 5 and 10 m) to adult individuals have allelopathic effects on seed germination. However, the effect varied among different distances and forest litter aqueous extracts concentrations. Forest litters collected from canopy 5 m distance have the strongest allelopathic effects on seed germination percentage and germination index. When the concentration of forest litter aqueous extracts reached to 2%, seed germination percentage and germination index decreased to 77.33% and 21.35, respectively. These indictors significantly reduced 18.32% and 20.5% compared to control, respectively. (3) The aqueous extracts of moss which collected under the plant canopy also inhibited seeds germination percentage of R. protistum var. giganteum. Based on above results, we concluded that the plant has autotoxicity effects on its seed germination, which may further influence its natural regeneration. The forest litters also have inhibited allelopathic effects on seed germination. Thus, we can reasonable to assume that the autotoxicity and allelopathic effects would affect the natural regeneration of R. protistum var. giganteum populations.