Controlled synthesis of tunable Mn-iron-oxide (Mn-FeOx) hybrids with unique three-dimensional (3D) porous structure based on diatoms for high performance supercapacitors is demonstrated. Successful transition process from MnO2 to FeOOH on diatomite was performed by two-step hydrothermal method and resultant replicas with 3D diatom morphology were obtained via etching process. The fabricated MnFeOx-0 diatom replica without transition was composed by MnO2 nanosheets and exhibited a high specific capacitance (228.6 F g(-1) at 1 A g(-1)), good rate capability (74.6% retention after current density were increased to 10 A g(-1)), high coulombic efficiency (about 93.1% at 10 A g(-1) ), and steady cycling performance (94.3% capacitance retention after 4000 cycles). MnFeOx-110 replica with FeOOH nanorods owned 224.6 F g(-1) at 1 A g(-1), high coulombic efficiency about 80% at 10 A g(-1) and steady cycling performance about 92.5% retention after 4000 cycles. Finally, an asymmetric supercapacitor was assembled based on MnO2 nanosheets as the positive electrode and FeOOH nanorods as the negative electrode, which delivered a wide potential of 2 V with maximum energy density of 51.5 Wh kg(-1) and power density of 9.1 kW kg(-1). Considering that the two replicas owned great energy storage property, it opens an opportunity for rational design of the diatom morphology samples applied to high-performance supercapacitors.