Based on the radiation transfer model, the remote sensing reflectance dataset is simulated under different vertical distributions of chlorophyll-a and suspended particle. In order to study the influence of vertical distribution to the remote sensing retrieval algorithm precision, the dataset is supplied to check the retrieval model of chlorophyll-a, suspended particle and inherent optical properties. The results indicate that the overestimate of suspended particle band ratio model is greater than single band model under the effect of suspended particle and chlorophyll-a vertical distribution. Chlorophyll-a band ratio and three-band model can reduce the overestimation of chlorophyll-a induced by the suspended particle and chlorophyll-a vertical distribution. The suspended particle and chlorophyll-a vertical distribution have double effects on the inherent optical properties retrieval model. Namely, the suspended particle vertical distribution will lead to overesitmate the absorption and backscattering coefficient, while the chlorophyll-a vertical distribution will lead to underestimate. The results of inherent optical properties retrieval model is uncertain under the double effects of suspended particle and chlorophyll-a.