The invention discloses a method for ecological afforestation on tropical coral reefs and islands, which comprises the following steps: (1) cultivating and selecting seedlings: planting seedlings of cerbera manghas, calophyllum inophyllum and clerodendrum inerme into nonwoven-cloth bags containing culture substrate; the roots and stems of cynodon dactylon are selected and kept wet; all these seedlings are of healthy state; (2) digging planting pits for seedlings: the sand fields of reefs or islands are leveled; planting pits of cerbera manghas seedlings and calophyllum inophyllum seedlings are 0.5m in length, width and height, with 1.5m of spacing from each other, and adjacent planting pits are arranged in a triangular pattern; at the center of every adjacent four planting pits of tree seedling, the planting pits of clerodendrum inerme is dug, with 0.3m in length, width and height; (3) planting the seedlings in the pits. The invention discloses a method for ecological afforestation on southern tropical coral reefs and islands by using indigenous plants. The method is simple, easy, economical, effective and fast when afforesting the man-made reefs and islands.