Abstract: Objective To evaluate the effects of standard and individualized procedures to radiofrequency ablation (RFA) of primary liver cancer. Methods From June 2004 to June 2012, 562 patients with primary liver cancer treated with RFA were retrospectively analyzed. At the same time the clinic data of 574 cases about the partial hepatectomy were taken as control group. Postoperative recovery, surgical complications, tumor residual or recurrence, postoperative overall survival and postoperative tumor-free survival were observed. Results Two groups were no dead cases. RFA group was significantly lower than the surgical resection group in the mean postoperative hospital stay and the average cost of hospitalization (P ＜ 0.001; P = 0.041). There were no serious complications in RFA group, and its liver dysfunction was mainly mild or moderate degree. Furthermore RFA group was significantly lower in the level of liver function damages than surgical resection group (P ＜ 0.001). There were no residual tumor cases in surgical resection group after 1 month of operation, as well as 23 patients (41 tumors) was found residual tumors in RFA group. Two groups had no difference in postoperative 1-, 3-, and 5-year overall survival rate, and the surgical resection group was significantly higher than the RFA group in postoperative 1, 3, and 5 year tumor-free survival rate (P = 0.024). Conclusions Not can only RFA completely destroy the tumor but it has also rapid postoperative recovery and fewer complications. RFA would have the similar effects with surgical resection if the treatment is appropriate, but it has lower tumor-free survival rate than surgical resection. Therefore standard and individualized program is the key factor to improve RFA long-term efficacy in treating primary liver cancer.