The design of three-dimensional (3D) nanoarchitectures on a flexible substrate has emerged as a novel strategy for fabricating cutting-edge wearable and portable power sources. Herein, we propose a simple and versatile approach towards the fabrication of hierarchical nanoporous manganese nickel selenide (MnxNi1-xSe2) and manganese iron selenide (MnxFe1-xSe2) nanosheets as positive and negative electrodes for flexible charge storage devices to achieve ultra-high energy density. The Mn substitution into Ni/Fe-selenide results in hierarchical architecture with highly altered electronic structure, offering enhanced electrical conductivity, increased catalytic activity, and improved stability of Ni/Fe phases upon cycling. Under optimized conditions, the Mn0.33Ni0.67Se2 and Mn0.33Fe0.67Se2 electrodes showed high specific capacities of ∼333 and 251 mAh g−1 at a current density of 1 mA cm−2, superior rate capabilities of 81.4 and 80.9% capacity retention at 50 mA cm−2, respectively, and outstanding cycling stability. Most importantly, in flexible solid-state assembly, the Mn0.33Ni0.67Se2//Mn0.33Fe0.67Se2 based SC delivers the excellent energy density of 87.2 Wh kg−1 at a power density of 0.672 kW kg−1, along with ultra-long durability of 96.2% capacity retention after 10,000 cycles at 30 mA cm−2. Thus, it would be believed this new fabrication strategy certainly promising for flexible electronics devices in the near future.