[Pr0.7Sr0.3MnO3/La0.5Ca0.5MnO3]20 superlattices were epitaxially fabricated on (001) MgO substrates with 24 nm La0.5Ca0.5MnO3 (LCMO) buffer layer by pulsed laser deposition. As the thickness of Pr0.7Sr0.3MnO3 (PSMO) layer and LCMO layer is not identical, non-uniformity in the superlattice period thickness will occur and result in lower metal–insulator transition temperature and larger magnetoresistance (MR) at a wide low-temperature range. Furthermore, the percolation model was used to quantitatively understand the transport mechanism of superlattice. Our research results demonstrate that inhomogeneous layer thickness accompanied with charge ordering phase separation can strongly influence the transport properties of superlattice. Enhanced magnetoresistance at a wide temperature range provides possibilities for practical application in manganite-based film devices.