To investigate the relation between the dynamic counts of Circulating Tumor Cells (CTCs)/Circulating Tumor Microembolis (CTMs) in peripheral blood and the prognosis of local advanced nasopharyngeal carcinoma (NPC). Methods Thirty-eight local advanced NPC patients were enrolled. Blood was collected at time points of before treatment, after neo-chemotherapy, 1 month and 1 year after intensity modulated radiotherapy (IMRT), respectively. CTCs/CTMs were detected by differential enrichment-tumor marker immunofluorescence staining-fluorescence in situ hybridization (SE-iFISH) method. Besides the relations among baseline CTCs/CTMs, clinicopathological features, serum EBV-DNA expression level and radiotherapy target parameters was analyzed, finally the relationship among CTCs, CTMs and prognosis was detected.Results The positive rates of CTCs and CTMs before treatment were 94.74% (36/38) and 10.53% (4/38), respectively, in which 2 patients presented PD-L1 (2/38).No significant differences among CTCs/CTMs baseline, gender, age, ECOG score, TNM stage and serum EBV-DNA expression in local advanced NPC patients were detected(P=0.337, P=0.502, P=0.090, P=0.076, P=0.398, respectively),and no relation among CTCs/CTMs baseline and primary tumor target (GTVnx), lymph node target (GTVnd) and gross tumor volume (GTV) were found (P=0.478, P=0.647, P=0.077; P=0.254, P=0.687, P=0.082, respectively). Meanwhile, in total, 20 patients (DCR=85% and PD rate=15%) was obtained in follow-up. The number of CTCs and CTMs were (9.8±5.7) and (2.9±1.2) before treatment and decreased to (2.4±6.2) and (1.4±0.2) after treatment, respectively. Furthermore, not only the number of CTCs and CTMs of 3 PD patients was (14.2±3.9) and (2.9±1.2) before treatment and decreased to (3.7±4.2) and (1.4±2.2) after treatment, respectively, but also the CTCs/CTMs ratio and PD-L1 positive on CTCs decreased, especially was triploid, tetraploid and ≥pentaploid CTCs subtype.Conclusion Monitoring peripheral blood CTCs, CTMs and CTCs/CTMs ration could be a prognosis potential indicator of local advanced NPC.