In this paper an ionic liquid 1-hexylpyridinium hexafluorophosphate based carbon ionic liquid electrode (CILE) was fabricated and used as the basal electrode, which was further modified by graphene (GR) and ZrO2 nanoparticle with chitosan (CTS) film to immobilize the nanocomposite. The modified electrode was denoted as CTS–GR–ZrO2/CILE and further used for the simultaneous detection of adenosine and guanosine. Electrochemical performances of the modified electrode were greatly enhanced due to the presence of GR–ZrO2 nanocomposite, and the direct electro-oxidation behaviors of adenosine and guanosine were carefully investigated. Both adenosine and guanosine exhibited an increase of the oxidation peak currents with the negative shift of the oxidation peak potentials on the modified electrode, which indicated the electrocatalytic activity of GR–ZrO2 nanocomposite on the electrode surface. Electrochemical parameters of adenosine and guanosine on CTS–GR–ZrO2/CILE were calculated respectively, and a new electroanalytical method for the simultaneous determination of adenosine and guanosine was further established with the peak-to-peak separation (ΔEp) as 0.225V. The proposed method was successfully applied to detect adenosine and guanosine in human urine samples with satisfactory results.