Transparent conductive oxides (TCOs) have attracted significant attention due to their high electrical conductivity and optical transparency, which are crucial for modern optoelectronics. Among TCOs, indium tin oxide (ITO) stands out for its superior properties and wide range of applications. The performance of ITO is heavily influenced by the fabrication process and the level of tin oxide (SnO2) substitution. In this work, we systematically investigated the electron transport behavior of amorphous and crystalline ITO films as a function of SnO2 content. In amorphous films, stable electron transport was observed across the entire substitution range, owing to the homogeneous distribution of indium and tin. In contrast, crystalline films exhibited a transition from epitaxial to polycrystalline states due to lattice mismatch, leading to a significant decline in electron transport properties. By analyzing thermopower and resistivity variations through percolation theory, we identified phase separation between In2O3 and SnO2, confirmed by x-ray photoelectron spectroscopy and visualized through conductive atomic force microscopy. Our findings indicate that electron scattering at incoherent grain boundaries plays a dominant role in degrading the transport properties of crystalline ITO films. These insights are expected to guide future advancements in TCO-based materials and devices.