The primary goal of this research is to investigate the clinical effect of transforaminal endoscopic spine system in the treatment of lumbar disc protrusion with vacuum phenomenon. A total of 124 patients with lumbar disc protrusion underwent transforaminal endoscopic spine system, including 85 patients with the non-vacuum phenomenon and 39 patients with the vacuum phenomenon, were retrospectively collected. VAS score,JOA score, improvement rate, and safety evaluation of patients with different signs were compared. Results showed that after the surgery, the VAS score decreased from (7.52±1.02) to (3.44±0.97) in vacuum phenomenon group (t=3.574 9, P=0.021), and from (7.35±0.99) to (2.51±0.85) in the non-vacuum phenomenon group (t=7.112 5, P<0.001). JOA score in the vacuum phenomenon group increased from (11.79±1.98) to (14.72±1.66)(t=2.075 8, P=0.195) in three monthes, and the non-vacuum phenomenon group increased from (12.21±2.01) to (19.25±1.57) (t=9.774 5, P<0.001). Postoperative C-reactive protein level, intraoperative blood loss, 24 h postoperative drainage volume, complication rate, and recurrence rate were all higher in vacuum phenomenon group. In conclusion, the transforaminal endoscopic spine system can effectively treat lumbar disc protrusion, but for patients with the vacuum phenomena, there may be long-term lumbar pain. Molecular dynamics simulations between IGFBP6 and IGF were performed, which gives us more information for the investigation of the pathogeny of the lumbar disc protrusion.