Nitrogen and carbon stable isotope values can be used to obtain eco-physiological information on macrophytes. This study collected macrophytes at different seasons from Gonghu Bay and Meiliang Bay of Lake Taihu, China to determine the variations of stable isotope values with regard to different season, space and species. The results showed that, with the season, space and species changing, nitrogen and carbon stable isotope values of macrophytes were changed, and the changed values were not obvious with seasonal variation in general, but had certain regularity with the space changes. The nitrogen stable isotopes of Myriophyllum spicatum, Potamogeton malaianus, Vallisneria natans and Eichhornia crassipes in Meiliang Bay were significantly higher than those of Gonghu Bay. The nitrogen stable isotope from emergent plants of Phragmites communis showed higher level in Meiliang Bay than that in Gonghu Bay. However, the carbon stable isotope values of Myriophyllum spicatum and Vallisneria natans in Gonghu Bay were significantly higher than those in Meiliang Bay, others were not significant in the differences. In Gonghu Bay and Meiliang Bay, the carbon stable isotope values of floating plants and emergent plants were lower in Phragmites communis, Eichhornia crassipes and Trapa incise, while Potamogeton maackianus, Ceratophyllum demersum, Potamogeton malaianus, Vallisneria natans, Elodea nuttallii and Myriophyllum spicatum of submerged plants were higher. This might due to the different environments and carbon sources.