In-plane micro-supercapacitor (MSC) is an important energy storage equipment for the power-source backup in miniaturized electronics. Covalent organic framework (COF) with the regular porous structure and high stability is emerging as a promising flexible MSC electrode material. Herein, the large-area shape-customizable COFTAPB-DHPA free-standing nano-film with the thickness of ∼11 nm was prepared via the surfactant-monolayer-assisted interfacial synthesis (SMAIS) method, followed by space-partitioning (covalent bond with ionic liquid, IL-COFTAPB-DHPA) and metal coordination (Co2+, Co-COFTAPB-DHPA) two strategies to enhance the capacitance performances. The MSC-COFTAPB-DHPA, MSC-IL-COFTAPB-DHPA and MSC-Co-COFTAPB-DHPA were fabricated directly by using corresponding as-prepared COF films as flexible electrodes. The maximum energy density value of MSC-IL-COFTAPB-DHPA (139.7 mWh/cm3) and MSC-Co-COFTAPB-DHPA (230.4 mWh/cm3) is 106% and 240% higher than the reported highest value in the reported two-dimensional (2D) material based MSCs at this stage, respectively. This work provides the potential MSC application direction of the large-area and crystalline 2D-COF nano-film.