In this work, p-MoO3 nanostructures/n-TiO2 nanofiber heterojunctions (p-MoO3/n-TiO2-NF-HJs) were obtained by a two-step fabrication route. First, MoO2 nanostructures were hydrothermally grown on electrospun TiO2 nanofibers. Second, by thermal treatment of the obtained MoO2 nanostructures/TiO2 nanofibers, p-MoO3/n-TiO2-NF-HJs were obtained due to the phase transition of MoO2 to MoO3. With increasing the concentration of molybdenum precursor in hydrothermal process, the morphologies of MoO2 changed from nanoparticles to nanosheets, and then fully covered shells with an increased loading on TiO2 nanofibers. After calcination, the obtained p-MoO3/n-TiO2-NF-HJs possessed similar morphology to that without thermal treatment. X-ray photoelectron spectra showed that both Ti 2p and OTi-O 1s peaks of p-MoO3/n-TiO2-NF-HJs shifted to higher binding energies than that of TiO2 nanofibers, suggesting electron transfer from TiO2 to MoO3 in the formation of p-n nanoheterojunctions. The p-n nanoheterojunctions decreased photoluminescence intensity, suppressed photogenerated electrons and holes recombinations, and enhanced charge separation and photocatalytic efficiencies. The apparent first-order rate constant for the degradation of RB by p-MoO3/n-TiO2-NF-HJs with nanosheets surface morphology was two times that of TiO2 nanofibers. For the core/shell structure of p-MoO3/n-TiO2-NF-HJs, the internal electric field of p-n junction forced the photogenerated electrons transferring to TiO2 cores, then decreased the surface photocatalytic reactions and led to the lowest photocatalytic activity among the p-MoO3/n-TiO2-NF-HJs.