Twelve aaptamine derivatives were isolated from the South China Sea sponge Aaptos suberitoides. The structures of all compounds were unambiguously elucidated on the basis of NMR spectroscopic and comparison with the literature data. Compounds 1-5 shared an imidazole-fused aaptamine moiety, among which 2 and 3 were the first discovery of halogenated aaptamine alkaloids. Compound 1 were a complex of 5 and 8. Moreover, both of 5 and 8 have two kinds of conjugation forms. All compounds were evaluated in cytotoxic and bone metabolism assays. Compound 7 played a two-way regulation function in the balance of bone metabolism,which can promote the proliferation and differentiation of osteoblasts, but also inhibit the differentiation of osteoclasts.