Objective The objective is to study the effect of individual N-glycosylation sequon on Suc2 activity and stability, and improve inulin conversion capacity and ethanol production of yeast by manipulating the key N-glycosylation sequon in Suc2. Results Based on previous reported data, it could be deduced that both the activity and thermal stability of Suc2 are probably influenced by some key N-glycosylation sequons. Thus, totally 13 N-glycosylation residues of Suc2 were individually deglycosylated by site-directed mutagenesis. Fermentation results indicated that deglycosylation at N4, N78 and N146 sequons improved Suc2 activity and ethanol production of host strains, whereas deglycosylation at N45 showed an opposite effect. Carbohydrate depletion of Suc2 N4 especially endowed the host strain with better ethanol fermentation performance from inulin when the strain was cultured under the higher temperature for 48 h, indicating that deglycosylation of N4 might improve the thermal stability of the Suc2. Conclusions Carbohydrate chains at N4, N45, N78 and N146 played an important role in modulating Suc2 activity and inulin catabolism of the S. cerevisiae strain. These key N-deglycosylation sequons should become potential targets for rational engineering of S. cerevisiae strains to enhance the ethanol production from inulin.