Comparative evaluation of biodiversity conservation effectiveness is significance to implement the transfer payment policy of ecological compensation reasonably, as to promote the effective improvement of the national ecological conservation management level. In this study, the important ecological function areas for biodiversity conservation, which originated from the National Ecological Function Zoning during 2015, were used for spatially comparative assessment. The conservation effectiveness structure index was established to explore the regional differences of biodiversity conservation effectiveness in important ecological function areas. The results showed that:(1) the structural reference of important ecological function areas in the South China, East China and Central China was better than the Northeast, and important ecological function areas in the Northwest and Southwest were the worst, which illustrated the regional diversity of the national ecological environment; (2) the conservation effectiveness structure index of important ecological function areas in the Northwest and Southwest was better than that of the Central China and South China, while the Northeast and East China were lower, which reflected the spatial differences in biodiversity conservation effectiveness in important ecological function areas in 2015; (3) from the perspective of the conservation effectiveness structure index of grassland, forest and wetland biodiversity, the important ecological function areas in the Northwest and Southwest, Northeast and Southwest, East China had great advantages respectively. The results provide the spatial differences of the biodiversity conservation effectiveness in important ecological function areas, and provide a reference for the government to improve ecological compensation mechanisms and formulate ecosystem restoration plans.