The isomerization of glucose to fructose is the rate determining step in many techniques for chemo‐catalytic conversion of cellulosic biomass to highly value‐added biochemicals. However, current techniques are generally challenging by poor process efficiency, low fructose yield and selectivity, etc. Therefore, the exploitations of novel catalytic systems for the efficient isomerization of glucose are important and highly desired. Herein, a series of biodegradable guanidinium ionic liquids were synthesized and employed in the selective isomerization of glucose to fructose. The results demonstrated that the performance of the isomerization of glucose was significantly influenced by the basic strength of the ionic liquids and the reaction conditions involving catalyst dosage, reaction temperature, time, and solvent. At the optimized conditions of 80 °C for 30 min, an impressive fructose yield of 34.1 % could be obtained in the presence of tetra methyl guanidinium proline ([TMG]Pro). Furthermore, the kinetic behavior of the process was further studied, and the apparent activation energy was 57±2 KJ/mol, which is lower than most current base‐catalyzed glucose isomerization systems. Moreover, the results of isotope labeling experiments showed that this aqueous isomerization of glucose was proceeded via a deprotonation mechanism. Therefore, this work provides a new insight on the selective isomerization of glucose.