Objective To explore the clinical significance of Nano-Carbon particles and 3D laparoscopy in central compartment lymph node dissection and parathyroid glands protection in treatment of cN0 thyroid cancer. Methods We conduct a retrospective analysis of sixty-five patients with cN0 thyroid cancer who were received 3D laparoscopic thyroidectomy in the last 3 years. All patients were received total resection of thyroid plus the affected side and (or) contralateral side central compartment lymph node dissection. All patients were allocated to control group (n = 32) and carbon nano-particles trace group (tracer group, n = 33). The lymph node-related indexes (including number of dissected lymph node at Ⅵ area, number of Metastatic lymph node and Frozen lymph node-positive rate at Ⅵ area), serum calcium (24 h after surgery) and PTH (48 h after surgery) were collected and compared between the 2 groups. Results Number of dissected lymph node at Ⅵ area, positive rates of intraoperative frozen-section examination of parathyroid glands and PTH (48 h after surgery) were found statistical higher in nanoparticles group than control (P < 0.05). No statistical difference were found in Number of Metastatic lymph node and serum calcium (24 h after surgery) (P < 0.05). Conclusion The clinical significance of carbon nanoparticles and 3D laparoscopy is effective and feasible for central compartment lymph node dissection and parathyroid glands protection in treatment of cN0 thyroid cancer.