Heparin (HP) has enormous potential for clinical medication applications owing to its anticoagulant activity. However, the strong anticoagulant capacity of HP also leads to some side effects. Herein, a photocaged derivative (HP-DMNB) of HP was synthesized for light control of its anticoagulant activity. The synthesized HP-DMNB was characterized by NMR and FTIR analysis, which confirmed the successful modification of HP with the photocleavable 4,5-dimethoxyl-2-nitrobenzyl (DMNB) groups. After the modification, the molecular weight of HP-DMNB (DS = 0.34%) changed from 61 to 71 kDa. Anticoagulant activity analysis showed that HP-DMNB had a reduced anticoagulant capacity compared with commercial HP, while its anticoagulant activity will regain after releasing the free carboxyl groups of HP under UV light. In addition, HP-DMNB and its UV irradiated products were observed to possess good biocompatibility through the MTT assays and live-dead assays with HaCaT cells, which may have impacts on the clinical medication applications of HP.