The present invention relates to a hydrogenation and residual carbon removing catalyst, which contains an active metal component and a modified hydrogenation catalyst carrier, wherein the modified hydrogenation catalyst carrier preparation method comprises: repeatedly and sequentially performing impregnating and drying on a carrier being subjected to hydrothermal treatment, and calcining the finally obtained dried product. The invention further provides a preparation method and applications of the hydrogenation and residual carbon removing catalyst. According to the present invention, by using the hydrogenation and residual carbon removing catalyst, the high removal rate of nitrogen, sulfur and heteroatoms and the high residual carbon removal rate in the heavy oil hydrotreating can be obtained, and the high asphaltene removal effect can be provided.