The purpose of this study was to analyze the effect of strontium-substituted hydroxyapatite (Sr-HA) on bone osseointegration of the implants using fluorescence microscopy. We allocated 20 implants to two groups: Sr-HA group and HA group. Electrochemically deposited HA and Sr-HA coatings were applied onto the implants separately. All the implants were inserted into femur bone of rabbits. Oxytetracycline hydrochloride, alizarin-complexon, and calcein green were respectively administered 7, 28, and 46 d after the implantation. After eight weeks, femurs were retrieved and prepared for the fluorescence microscopy observation. We analyzed the bone mineral apposition rates (MARs), bone area ratios (BARs), and bone to implant contact (BIC) of the two groups. Fluorescence microscopic observation showed that all groups exhibited extensive early peri-implant bone formation. The MAR of the Sr-HA group was greater than that for pure HA from 7 to 28 d after implantation, but no significant difference was found at later stage. And the BIC showed difference at 7 and 28 d compared with pure HA. We concluded that Sr-HA coating can improve the bone osseointegration of the implant in the early stage compared with the HA coating.