Objective This study aims to assess the clinical effects of HyFlex CM instruments on root canal preparation. Methods A total of 300 mandibular first molars and second molars that required endodontic treatment were selected and randomly divided into two groups, namely, the HyFlex CM and Protaper groups. The root canals were prepared with HyFlex CM instruments in the HyFlex CM group and with Protaper in the Protaper group. The root canal preparation time, incidence of pain after root canal preparation, effects of canal obturation, and incidence of instrument separation were compared by using the χ2 test. Results The average root canal preparation time in the HyFlex CM group was 21.7 min, whereas that in the Protaper group was 22.5 min(P>0.05). The incidence rate of postoperative pain in the HyFlex CM group was 4%, whereas that in the Protaper group was 3%(P>0.05). Adequate root canal filling in the HyFlex CM group was 95.10%, whereas that in the Protaper group was 96.18%(P>0.05). Instrument separation in the HyFlex CM group was 1, whereas that in the Protaper group was 6. Conclusion HyFlex CM instruments can reduce the incidence of postoperative pain, as well as maintain a satisfactory anatomical shape of the root canal while significantly decreasing instrument separation. These conditions can improve filling effect and quality.