To describe the applications and effects of electromagnetic navigation (EN) technology in distal locking for the treatment of long diaphyseal fracture (LDF) with interlocking intramedullary nailing (IIN). An interventional study. The Second Affiliated Hospital of Soochow University, China, from March 2013 to July 2014. Patients who underwent IIN-LDF were selected. Twenty-four (50%) of whom were operated under EN guidance (group A) and the other 24 (50%) under conventional targeting guidance (group B). The distal locking time and X-ray irradiation time of the two groups were compared. Each group included 16 (33.3%) cases of femoral fracture and 8 (16.7%) cases of tibial fracture. The success rate of distal locking in group A was higher than that in group B (95.8% vs. 83.3%, p=0.045). There were statistically significant differences in the distal locking time and X-ray irradiation time of femoral intramedullary nailing between the two groups (p=0.027 and p=0.001, respectively). There were no statistically significant differences in the distal locking time and X-ray irradiation time of tibial intramedullary nailing between the two groups (p=0.347 and p=0.056, respectively). EN-IN was advantageous as it enabled easy targeting, significantly reduced intraoperative fluoroscopy and operation time and small trauma and had other advantages when used for treating LDFs, especially femoral diaphyseal fractures.