A CEC method is described for the simultaneous determination of 11 nucleosides and nucleobases including cytosine, uracil, uridine, hypoxanthine, 2′-deoxyuridine, inosine, guanosine, thymidine, adenine, adenosine, and cordycepin in Cordyceps using 5-chlorocytosine arabinoside as internal standard (IS). Chemometric optimization based on central composite design was employed to find the optimum conditions. The factors for optimization were defined as three parameters: voltage, pH, and concentration of ACN as organic modifier. The resolution (Rs) between inosine and guanosine, as well as the entire run time were employed to evaluate the response function. A running buffer composed of 4 mM ammonium acetate and 2 mM triethylamine (TEA) adjusted to pH 5.3 using acetic acid, and containing 3% ACN as modifier, with gradient voltage (0-4 min: 20 kV, 4-12 min: linear gradient from 20 to 30 kV; 12-16 min: 30 kV) were found to be the optimum conditions for the separation. Separation of the 11 investigated compounds and 5-chlorocytosine arabinoside was achieved within 16 min. The contents of the 11 compounds in natural and cultured Cordyceps sinensis, and cultured Cordyceps militaris were also compared. The result showed that CEC is an efficient method for analysis of nucleosides and nucleobases in Cordyceps, which is helpful to control the quality of this valued traditional Chinese medicine.