Ultrathin superconducting Nb films of about 8 nm thick have been deposited on heavily doped Si substrates through DC magnetron sputtering and then the high-quality Nb/Si superconductor-semiconductor heterojunctions have been fabricated by electron beam lithography and reactive ion etching technology. An abnormal magnetoresistance effect, which manifests as a zero field resistance peak under the magnetic field applied perpendicular to the heterojunction interface, has been distinctly observed when the Nb film is in the superconducting state. By considering the heterojunction interface being equivalent to the structure of superconductor-barrier layer-superconductor configuration, we could generally understand this unusual effect based on the Andreev reflection microscopic mechanism. In addition to the significant value in fundamental research, our results can be of some help for the future development on compatibility and scalability of the silicon-based nanoscale superconducting devices for integrated circuits and superconducting quantum electronics.