As a malignant disease that seriously threatens human health, hepatocellular carcinoma (HCC) lacks effective early screening and prognostic assessment methods. Herein, we developed a method for efficient capture and multi-phenotype analysis of circulating tumor cells (CTCs) of hepatocellular carcinoma. Anti-ASGPR antibody and anti-EpCAM antibody were modified in parallel on a deterministic lateral displacement (DLD)-patterned microfluidic Synergetic-Chip to enhance capture efficiency by a complementary effect. CTCs were detected in 45 out of 45 (100%) of HCC patients, with sensitivity and specificity of 97.8% and 100%, respectively. Patients with more total CTCs and non-epithelial CTCs were in later stages of HCC and more malignant progression. This strategy proposes a feasible approach for early diagnosis and prognosis of hepatocellular carcinoma.