Objective Tocompare the effects between ultrasound-guided percutaneous microwave ablation and CT ultrasound-guided radiofrequency ablation in treating primary liver cancer. Methods Forty-six patients (72 lesions) with primary liver cancer treated by minimal invasive interventional therapy in our hospital between February 2009 and March 2013 were selected as study subjects and were equally divided into study group and control group by the random number table method. The control group received ultrasound-guided percutaneous microwave ablation while study group received CT ultrasound-guided radiofrequency ablation. The related perioperative indexes (operation time, postoperative length of stay, hospitalization expenses), state of ablation (ablation count, duration of ablation), imaging evaluation of clinical efficacy, 3 year follow-up recurrence rate in the two groups were observed. Results Operation time and postoperative length of stay of study group were significantly shorter than control group (P＜0.05). There was no significant difference in hospitalization expenses between the two groups (P＞0.05), after operation, lesions in both groups were effectively removed. The 3-year recurrence rate in study group was significantly lower than control group (χ2 =5.254, P＜0.05). Conclusion Clinical efficacy of both ultrasound-guided percutaneous microwave ablation and CT ultrasound-guided radiofrequency ablation are significant in treating primary liver cancer. Radiofrequency ablation has more advantages in operation time, length of stay, duration of ablation and 3-year recurrence rate.