The thermal shrinkage and its stress of poly(ethylene terephthalate-isophthalate) copolyester multifilament were investigated in terms of crystallinity and molecular orientation. Central composite design was used to determine the number of experiments. The thermal shrinkage increased with isophthalic acid content and this phenomenon was explained in terms of crystallinity. The thermal shrinkage decreased but peak shrinkage stress increased with the increase of draw ratio. This phenomenon was related to the strain-induced crystallization. Both the thermal shrinkage and peak shrinkage stress decreased with the increase of drawing temperature and this phenomenon was due to the molecular orientation of the copolyester.