2,4-Difluoro-3-formyl-phenylboronic acid (DFFPBA)-modified magnetic attapulgite (ATP-Fe3O4-NH2-DFFPBA) was synthesized and employed to capture and enrich cis-diol-containing biomolecules. The resulting material exhibited a high saturation magnetization value of 20.71 emu/g, allowing the absorbent to be conveniently magnetically separated. Combining the Fe3O4 nanoparticles with the high specific surface area of attapulgite yielded a material with a high capture capacity (13.78 mg/g) for adenosine. Furthermore, ATP-Fe3O4-NH2-DFFPBA was found to possess remarkable selectivity for adenosine at a low molar ratio of adenosine/2-deoxyadenosine (1:500). The potential applications of this material were explored by using it to extract five nucleosides from urine samples, and the results demonstrate that it can decrease matrix interference and selectively enrich analytes.