Venous thromboembolism (VTE) is a common coagulative dysfunctional complication of cancer patients. The present study aimed to determine the association and diagnostic values of serum homocysteine (Hcy) and folic acid levels with VTE in cancer patients. We enrolled 700 cancer patients and 100 healthy subjects in our study. All cancer patients, with or without VTE, underwent measurement of serum Hcy and folic acid levels and coagulative markers including D-Dimer, factor VIII, fibrinogen and tissue plasminogen activator. The diagnostic values of Hcy and folic acid were assessed by receiver operative characteristic (ROC) analysis. Correlations between Hcy and folic acid and coagulative factors were determined. Among the 700 patients with malignant tumors recruited in our study, a total of 89 patients had VTE combined within three months, and 611 patients did not have VTE. Cancer patients with VTE had significantly higher levels of Hcy and significantly lower levels of folic acid in serum. Both Hcy and folic acid in serum demonstrated high sensitivity and specificity in diagnosing VTE in cancer patients and showed strong correlations to coagulative markers. Hcy and folic acid, which have strong correlations to coagulative markers, are potential novel serum markers for stratifying VTE risk in cancer patients.