A hydrophilic basic polysaccharide, carboxymethyl chitosan (CMC) as a capillary coating is presented with a simple preparation procedure. The CMC-coated capillary showed a long lifetime of more than 100 runs, and had good tolerance to some organic solvents, 0.1 M HCL 0.1 M NaOH, and 5 M urea. The run-to-run, day-to-day, and capillary-to-capillary RSDs for the CMC-coated capillary were all below 2.0% for the determination of EOF. Moreover, the coatings with different concentrations and molecular weights of CMC were also investigated. The CMC-coated capillary was successfully applied to separate basic proteins and recombinant human erythropoietin (rhEPO). Furthermore, several experimental parameters, such as the concentration and pH of the running buffer, temperature, and applied voltage, were optimized for the separation of rhEPO glycoforms. Comparison of an uncoated capillary with chitosan- and CMC-coated capillaries for the separation of rhEPO glycoforms was also discussed. The results demonstrated that rhEPO glycoforms can be well separated by a CMC-coated capillary within 8 min with good reproducibility and resolution. Finally, the volatile BGE HAc-NH4Ac was utilized to separate rhEPO for its further application with CE-MS, achieving a satisfactory result.