Five morphological fractions (leaf blade, leaf sheath, stem, husk and cob) of stover of five maize genotypes, namely waxy, conventional, fodder, sweet and high-oil maize, respectively, were used to test the effects of genotype and morphological fractions on chemical composition and in vitro fermentation characteristics. The waxy maize had a higher (P < 0.05) stem but lower (P < 0.05) leaf blade proportion and fodder maize had a higher (P < 0.05) leaf blade but lower (P < 0.05) leaf sheath proportion than other genotypes, respectively. Maize genotype had a significant effect (P < 0.001) on the chemical composition of stover parts except for organic matter (OM) concentration. Chemical composition of stover parts was affected (P < 0.001) by morphological fractions. The interaction effects between genotype and morphological fraction on the fiber content of stover parts were significant. Over 0.40 and 0.50 of phosphorus (P) and crude protein (CP) of whole-plant maize stover were averagely contributed by leaf blade. Leaf blade, stem and cob contributed over 0.75 of OM, CP, P and fiber in the whole plant. There were significant effects of genotype and morphological fraction on both in vitro gas production parameters and in vitro organic matter disappearance of maize stovers. The genotype and morphological fraction of maize stover and their interaction had significant effects on NH3-N and total volatile fatty acid concentration and the molar proportion of volatile fatty acid in the supernatant after 72 h of incubation except for valeric acid. The present data indicated that the genotype and morphological fraction of maize resulted in variation in the nutritive value of maize stover.