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Ligand modulation on metal organic clusters endow them with different physical and chemical properties, while how ligand modulation further affects the electrochemical behavior of pyrolytic derivatives is still unclear. Herein, we constructed two trinuclear manganese clusters 1‐Mn3 [Mn3L12(Cl)2] [L1=N1,N3‐bis(3‐methoxysalicylidene) diethylenetriamine] and 2‐Mn3 [Mn3L22(C7H4O2)2] [L2=N1,N3‐bis(3‐salicylidene) diethylenetriamine] based on nitrogen‐rich Schiff‐base pentadentate ligands. The introduction of TG‐MS (thermogravimetry associated with mass spectroscopy) explores the difference and universality of the pyrolysis mechanism of two trinuclear manganese clusters, and divides the pyrolysis process into three Areas (Area I/II/III) according to temperature. Combined with other characterization techniques, the materials in these three areas were analyzed to explain the effect of ligand modification on the electrochemical properties of cluster pyrolysis derivatives. It is found that the Area III derivatives have the best capacitance performance, when the current density is 1 A g−1, the specific capacitance of 1‐900 is 1717 F g−1, and 2‐900 is 350 F g−1. By comparison of the phase evolution process and electrochemical performance of the two manganese clusters, it is proposed that the crumbling of the molecular structure and stacking mode of trinuclear manganese clusters during pyrolysis will affect the capacitive properties of the derivatives. This work provides a guidance for the differences of the properties of pyrolytic derivatives under ligand modulation. [ABSTRACT FROM AUTHOR]