The spectroscopic measurements of orthorhombic CaNb2O6 phosphor doped with Yb3+ ions have been performed. Low temperature spectra indicate that Yb3+ ions may occupy three types of nonequivalent sites inside the CaNb2O6 lattice: a main Yb3+ site dominating the near-infrared emission, and two other minor sites of similar behaviors to each other. An attempt to determine the Stark sublevels energies of the 2F7/2 and 2F5/2 manifolds of three Yb3+ nonequivalent ions was carried out. The fluorescence lifetimes associated to the emission lines of Yb3+ ions located at the main site and minor sites are also quite different. Furthermore, there exists energy transfer from the main site to the minor sites.