In-plane micro-supercapacitors (MSCs), as promising power candidates for micro-devices, typically exhibit high power densities, large charge/discharge rates, and long cycling lifetimes. The high areal/volumetric capacitances, high energy/power densities, high rate capability, as well as flexibility are the main scientific pursue in recent years. Among diverse electrode materials for MSCs, coordination polymer frameworks are emerging due to the designable porous structure and tunable functionality. However, the unsatisfied electrochemical performance still hinders their practical applications. In this work, we demonstrate the first time an efficient in-situ growth approach to precisely modify the vacancy of Prussian-blue nano-thin films with pyridine by coordination reaction for high energy-density MSCs. Confirmed by the experimental results and density functional theory calculation, the vacancy modification within Prussian-blue network improved the film-forming property, hydrophilicity, and electrochemical activity of the thin films. The resultant MSCs based on pyridine-modified Prussian-blue exhibited an ultrahigh energy density of up to 12.1 mWh cm−3 and an ultra-low time constant (τ0) of 0.038 ms, which are the best values among the state-of-the-art in-plane MSCs. This work provides an attractive solution for structural engineering of promising active materials on molecule level toward high-performance micro-energy devices.