This study presents a design of a 3D interface simulation model featuring an inverted pyramid structure. Our objective is to forecast the performance of GaN-based betavoltaic nuclear batteries with the PN junction 3D interface structures comparing a practical machining process. Initially, we computed the electron-hole pairs (EHPs) generation rate in GaN materials irradiated by both 63Ni and 147Pm sources using Geant4. Furthermore, we employed COMSOL Multiphysics, a finite element analysis software, to simulate the EHPs transport phenomena within the battery and investigate the influence of structural parameters on the output performance. Despite maintaining thicknesses of the P- and N-regions and consistent doping concentrations (Hp-GaN, Hn-GaN, Na, and Nd) as constants, the simulation results revealed notable disparities in the short-circuit current density (Jsc), open-circuit voltage (Voc), and maximum output power density (Pmax) among batteries irradiated with various radioactive sources. Subsequently, we investigated the output performance of the nuclear battery by altering parameters such as the number of inverted pyramid structures, junction depth, and type of radioactive source. Our investigation revealed that selecting 63Ni as the radioactive source, with Na at 1017 cm−3, Nd at 1014 cm−3, a junction depth of 0.1 μm, and inverted pyramid structures of 25, resulted in the following battery performance parameters: a short-circuit current density (Jsc) of 0.648 μA/cm2, an open-circuit voltage (Voc) of 2.3481 V, and a maximum output power density (Pmax) of 1.2949 μW/cm2. Substituting the radioactive source with 147Pm, the average short-circuit current density, Jsc, increased to 56.865 μA/cm2, and the maximum output power density, Pmax, increased to 94.975 μW/cm2, It's a significant enhancement in output performance.