A novel boronic acid functionalized magnesia–zirconia (ZM) based material was facile synthesized by Lewis acid–base chemisorption. The elemental analysis, inductively coupled plasma atomic emission spectrometer (ICP-AES) and Fourier transform infrared spectrometer (FT-IR) have proven the successful attachment of 3-aminophenylboronic acid derivative onto ZM surface. In the present work, the affinity of the resulting material towards cis-diols binding was evaluated by using it as the sorbent for solid-phase extraction of 4 nucleosides (namely cytidine, uridine, guanine and adenosine). The results show that such boronic acid modified magnesia–zirconia composite microparticles were excellent for capturing nucleosides in the system with a wide range of pH and high salt concentration, which could be effectively released using TFA–ACN–H2O (5 : 50 : 45, v/v/v) solution as elution. The 4 nucleosides spiked to untreated urine sample (i.e., no diluting or pH adjustment) were prominently enriched with recoveries in the range of 86–109% and LOD values in the range of 0.003–0.010 μg mL−1. The constructed calibration curves range from 0.05 to 2.0 μg mL−1 showing good linearity correlation coefficient (R ≥ 0.9961) and precision (RSD < 9%). The proposed material would allow for an alternative extraction strategy for identification and quantitative analysis of cis-diols structure compounds in biological samples.