Polymer dielectric capacitors are essential components in capacitive energy storage systems. However, their application in high-temperature environments remains limited due to reduced discharged energy density, primarily caused by decreased electrical breakdown strength and low dielectric constant of dielectric polymers at elevated temperatures. In this work, we present a molecular engineering strategy to address these challenges by tailoring the chemical structure of polyimide (PI) backbones. Through a systematic comparison of three structurally distinct PIs, we elucidate how chemical structure influence dielectric constant, electrical breakdown strength and overall energy storage performance. Incorporation of flexible ether linkages enhances the dielectric constant, while trifluoromethyl groups significantly boost electrical breakdown strength, achieving up to 644 MV/m at 200° C. As a result of this structural optimization, a discharged energy density of 4.53 J/cm3with over 90% charge-discharge efficiency is achieved at 200 ° C. These findings provide valuable guidance for the rational design of high-performance polymer dielectrics for high-temperature capacitive energy storage applications.