Slices of poly(glycolic acid) (PGA) extruded rods were characterized by wide angle X-ray scattering (WAXS) and small angle X-ray scattering (SAXS) using a synchrotron radiation light source, and the optimal annealing conditions of PGA rods after extrusion were studied to eliminate internal stress and improve the subsequent machinability of the rods. The WAXS results indicate that high temperature is more advantageous to the reduction of micro-strain, but the crystal grain size decreases with increasing annealing time at higher temperatures. The SAXS results indicate that high temperature is more conducive to decreasing the degree of orientation, and the effects of annealing time on the degree of orientation is significantly weaker than that of annealing temperature. The objective functions were established by integrating various data and analyzed through Response Surface Methodology. The results show that the optimal annealing conditions for PGA rods within the range of the experimental conditions studied are annealing at 200 ℃ for 2 h.