Porous hydroxyapatite (HAp) composite fibers functionalized with up-conversion (UC) luminescent and magnetic Na(Y/Gd)F-4:Yb3+,Er3+ nanocrystals (NCs) have been fabricated via electrospinning. After transferring hydrophobic oleic acid-capped Na(Y/Gd)F-4:Yb3+E,Er3+ NCs into aqueous solution, these water-dispersible NCs were dispersed into precursor electrospun solution containing CTAB. Na(Y/Gd)F-4:Yb3+,Er3+@HAp composite fibers were fabricated by the high temperature treatment of the electrospun Na(Y/Gd)F-4:Yb3+,Er3+ NCs decorated precursor fibers. The biocompatibility test on MC 3T3-E1 cells using MTT assay shows that the HAp composite fibers have negligible cytotoxity, which reveals the HAp composite fibers could be a drug carrier for drug delivery. Because the contrast brightening is enhanced at increased concentrations of Ge3+, the HAp composite fibers can serve as T-1 magnetic resonance imaging contrast agents. In addition, the composites uptaken by MC 3T3-E1 cells present the UC luminescent emission of Er3+ under the excitation of a 980 nm near-infrared laser. The above findings reveal Na(Y/Gd)F-4:Yb3+,Er3+@HAp composite fibers have potential applications in drug storage/release and magnetic resonance/UC luminescence imaging.