The effect of aging on the mechanical properties was investigated for a series of bacterial copolyester poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(3HB-co-3HH)] with 3HH molar fraction ranging from 5 to 18 mol %. The mechanism behind the aging phenomenon was studied by using gel permeation chromatography (GPC), differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS) in parallel to the tensile testing. It was found that the high initial crystallinity and the narrower amorphous region in the P(3HB-co-3HH) films are the key factors that cause the secondary crystallization in the aging process to embrittle the films of copolymers with 3HH fraction lower than 10 mol %. For the copolymers with 3HH fractions higher than 10 mol %, because of the intrinsically lower crystallinity and thicker amorphous region, the secondary crystallization cannot affect the mechanical properties significantly.