With the continuing construction of the new energy system, how to scientifically determine the absorption costs paid by the system for absorbing new energy and how to apportion the absorption costs fairly and reasonably are key to realizing the safe and economic operation of the power system. In response to the current challenges of measuring and reasonably allocating absorption costs of new energy, a method that takes into account the differences in regional power grids for the estimation and allocation of new energy absorption costs is proposed. First, a comprehensive method for estimating absorption costs of new energy based on energy storage investment planning is proposed. Using the Vickrey- Clarke-Groves (VCG) theory, a principle considering the positive and negative substitution benefits of absorption costs is further introduced to achieve comprehensive estimation and initial distribution of absorption costs. Secondly, a method for quantifying the differences in absorption capacity of different regional power grids based on flexible regulation capability characterization is proposed. Additionally, a method for reallocating absorption costs based on a comprehensive score of flexibility indicators is proposed, allowing regions with stronger absorption capacity to bear relatively lower absorption costs, thus ensuring a fair and reasonable allocation of absorption costs. Finally, the modified IEEE 14-bus system and an actual power grid are simulated and analyzed to verify the effectiveness of the proposed method.