〔Abstract〕 Objective To investigate the value of serum homocysteine (Hcy), alpha-fetoprotein (AFP) combined with carbohydrate antigen 199 (CA199) detection in the diagnosis of primary hepatocellular carcinoma (PHC). Methods A total of 52 patients with PHC group, 68 patients with benign liver disease (benign liver disease group) and 90 healthy people (control group) who underwent physical examination during the same period (control group) from May 2017 to June 2019 in the Affiliated Brain Hospital of Guangzhou Medical University were selected as research subjects. Serum Hcy, AFP and CA199 of the three groups were detected. The detection results of each index were observed, and the diagnostic efficacy of single and combined detection of each index was calculated. Results Serum Hcy, AFP and CA199 in PHC group were significantly higher than those in benign liver disease group and control group, and Hcy, AFP and CA199 in benign liver disease group were also significantly higher than those in control group, the differences were statistically significant (P < 0.05). The sensitivity, specificity, accuracy, positive predictive value and negative predictive value of combined detection were significantly higher than those of Hcy, AFP and CA199, with statistical significance (P < 0.05). Conclusion The levels of Hcy, AFP and CA199 in serum of PHC patients were significantly higher than those of benign liver disease patients and healthy people, the diagnostic efficacy of Hcy and AFP combined with CA199 was significantly higher than that of single index.