Abstract: Objective To investigate the difference clinical effects of unfractionated heparin, LMWH and fondaparinux in treatment of coronary syndrome. Methods 120 cases of patients with acute coronary syndrome were randomly divided into A, B, C three groups, 40 cases in each group. Group A was treated with heparin, group B were treated with low molecular weight heparin, and group C were treated with fondaparinux. The difference of endpoint primary treatment efficacy including major adverse cardiovascular events and bleeding in patients at 9 and 30 days between the three groups were analyzed. Results The main endpoint treatment effects at 9 days between three groups had no significant difference. The incidence of myocardial infarction in Group C at 30 days after treatment was significantly lower than that of group A and group B (P<0.05). The main and minor bleeding incidence rate in Group B and group C at 30 days after treatment were lower than that of patients in group A (P<0.01), but there was no significant difference between group B and group C (P>0.05). Conclusion The treatment efficacy of fondaparinux in coronary syndrome and is more safe, and might have clinical application value.