Objective To investigate the relationship of cerebral infarction with serum cystatin C (Cys C), matrix metalloproteinase-9 (MMP-9), and homocysteine (Hcy).Methods A total of 80 patients with cerebral infarction who were admitted to our hospital from January 2014 to June 2015 were selected as cerebral infarction group, and 30 healthy people who underwent physical examination in the same period were selected as control group. The levels of serum Cys C, MMP-9, and Hcy, as well as the size of lesion, and prognostic serum Cys C, MMP-9, and Hcy levels were all compared between the two groups.Results The cerebral infarction group had significantly higher levels of serum Cys C, MMP-9, and Hcy than the control group (P<0.05); convalescent patients with cerebral infarction had significantly lower serum Cys C and MMP-9 levels than patients in acute stage (P<0.05); convalescent and acute patients with cerebral infarction had similar Hcy levels (P>0.05). The levels of serum Cys C and MMP-9 in cerebral infarction group were positively correlated with the size of lesion (P<0.05), but the Hcy level showed no significant difference (P>0.05). Patients with good prognosis had significantly lower Cys C and MMP-9 levels than patients with poor prognosis (P<0.05), but the Hcy levels showed no significant difference (P>0.05). Multivariate logistic regression analysis showed that serum Cys C (OR=2.724, 95% CI:1.318-5.630), MMP-9 (OR=1.936, 95% CI:1.362-2.752), and Hcy (OR=4.915, 95% CI:1.372-17.607) were all risk factors for cerebral infarction.Conclusions The increased levels of Cys C, MMP-9, and Hcy are closely associated with the occurrence of cerebral infarction. Cys C and MMP-9 can also make the prognosis of patients with cerebral infarction, so they are of great significance in clinical practice.