The biodegradable porous composite scaffold, composed of poly(lactide-co-glycolide)(PLGA) and hydroxyapatite nanoparticles(n-HAP) surface-grafted with poly(L-lactide)(PLLA)(g-HAP)(g-HAP/PLGA), was fabricated using the solvent casting/particulate leaching method, and its in vivo degradation behavior was investigated by the intramuscular implantation in rabbits. The composite of un-grafted n-HAP/PLGA and neat PLGA were used as controls. The scaffolds had interconnected pore structures with average pore sizes between 137 μm and 148 μm and porosities between 83% and 86%. There was no significant difference in the pore size and porosity among the three scaffolds. Compared with n-HAP/PLGA, the thermo-degradation temperature(Tc) of g-HAP/PLGA decreased while its glass transition temperature(Tg) increased. The weight change, grey value analysis of radiographs and SEM observation showed that the composite scaffolds of g-HAP/PLGA and n-HAP/PLGA showed slower degradation and higher mineralization than the pure PLGA scaffold after the intramuscular implantation. The rapid degradation of PLGA, g-HAP/PLGA and n-HAP/PLGA occurred at 8–12 weeks, 12–16 weeks and 16–20 weeks, respectively. Compared with n-HAP/PLGA, g-HAP/PLGA showed an improved absorption and biomineralization property mostly because of its improved distribution of HAP nanoparticles. The levels of both calcium and phosphorous in serum and urine could be affected to some extent at 3–4 weeks after the implantation of g-HAP/PLGA, but the biochemical detection of serum AST, ALT, ALP, and GGT as well as BUN and CRE showed no obvious influence on the functions of liver and kidney.