The complex relationship between the molecular structure of ion-exchange resins and the elution of carbohydrates presents a challenge for the development of polymer materials for high-performance liquid chromatography under a wide range of conditions. We evaluated the effect of the number of methylene groups in the functional chain of the shell portion on carbohydrate separation. In particular, core-shell ion-exchange resins with a monomer weight ratio of 40:60 (denoted as St-60) were synthesized with a constant cross-linking degree of 40%. The number of methylene groups in the functional chain of the porous polymer shell was varied from two to six for analyses of carbohydrate separation performance under strong alkaline conditions. A mixture of inositol, glucose, fructose, and sucrose was separated using a 0.10 or 0.15 mol/L NaOH eluent at flow rates of 0.3–0.7 mL/min. As the number of methylene groups increased, the carbohydrate retention times for St-60(Me:4) at flow rates of 0.3–0.7 mL/min with 0.10 mol/L NaOH eluent increased slightly. The theoretical plate numbers of glucose and fructose at flow rates of 0.5 and 0.7 mL/min decreased as the number of methylene groups decreased from six to two. These results suggest that St-60 core-shell ion-exchange resins are highly efficient for carbohydrate analyses. Their suitability for strongly alkaline conditions allows their effective use in electrochemical detection.