The energy band alignment of a stacked Si/GaN heterostructure was investigated using X-ray photoelectron spectroscopy (XPS) depth profiling, highlighting the influence of the amorphous interface region on the electronic properties. The crystalline Si/GaN pn heterostructure was formed by stacking a Si nanomembrane onto a GaN epi-substrate. The amorphous layer formed at the stacked Si/GaN interface altered the energy band of the stacked heterostructure and affected the injection of charge carriers across the junction interface region. This study revealed the interfacial upward energy band bending of the stacked Si/GaN heterostructure with surface potentials of 0.99 eV for GaN and 1.14 eV for Si, attributed to the formation of the amorphous interface. These findings challenge the conventional electron affinity model by accounting for interfacial bonding effects. Electrical measurements of the stacked Si/GaN pn heterostructure diode exhibited a rectifying behavior, consistent with the XPS-determined energy band alignment. The diode outperformed early design with a low leakage current density of 5 × 10−5 A/cm2 and a small ideality factor of 1.22. This work underscores the critical role of the amorphous interface in determining energy band alignment and provides a robust methodology for optimizing the electronic performance of stacked heterostructures. The XPS-based approach can be extended to analyze and develop multi-layered bipolar devices.