Fructose is not only an important food and beverage ingredient, but also a renewable resource for production of bio-chemicals. In this paper, a series of N doped mesoporous carbon materials (MCNs) were prepared and evaluated as heterogeneous catalysts for catalytic isomerization of glucose to fructose. The MCNs were prepared through carbonization of p-phenylenediamine disulfate and the effects of desulfonation with NaOH and hydrogenation treatments were examined. It is found that the molar ratio of H2SO4/pPDA crucially affects the porous structure and the nitrogen content. Desulfonation with NaOH treatment could largely eliminate the sulfonic groups on the carbon edges and thus enhance the basicity of the MCN materials, whereas hydrogenation reduction could modify the N atom species and reinforce the strength of the basic sites, as a result enhancing the catalytic activities in glucose isomerization to fructose. Among all of the prepared MCN samples, MCN-2-DH showed an excellent activity in aqueous solution, which afforded a fructose yield of 31.6% with 84.6% selectivity.