Anion intercalation in graphite is deemed as a promising electrode chemistry in aqueous energy storage systems due to its high onset potential. Given the limited space in graphite, multivalent anions are favorable to achieve high specific capacity. However, relevant studies are scarce so that fundamental understandings of multivalent anion intercalation remain unclear. Herein, the intercalation behaviors of ClO4−, SO42−, and PO43− in graphite are systematically investigated. High capacity and interaction between anion and graphite are proved to be contradictory as the electric charge increases. As a result, ClO4− and SO42− intercalation exhibits promising performance in primitive graphite, while PO43− intercalation is much restricted due to the intensified electronic interaction. Two Zn–graphite dual‐ion batteries based on ClO4− and SO42− intercalations display high voltages of 1.85 V, and specific energies of 106 and 112 Wh kg−1. This work provides fundamental understandings of multivalent anion intercalation and guidance to fabricate aqueous batteries (ABs) with high energy density.