To compare the performance of magnetic bead (MB) and the concentrated precipitation (CP) based RT-qPCR to qualify cell free EBV DNA (cfEBV DNA) for nasopharyngeal carcinoma (NPC) in non-endemic area of China. From January 2014 to June 2024, a retrospective analysis of 2 cohort studies on cfEBV DNA in NPC patients was conducted to assess the diagnostic value, positive detection rate and clinical application. cfEBV DNA detection with CP based RT-qPCR in cohort 1 and MB based RT-qPCR method in cohort 2. The MB based RT-qPCR for the quantitative measurement of cfEBV DNA load was higher than the CP based RT-qPCR in the same plasma samples from NPC patients (P < 0.001). CP based RT-qPCR measured cfEBV DNA in 1405 NPC and 244 healthy controls in cohort 1 with 40.8% sensitivity (AUC = 0.704, 95% CI: 0.676-0.731). In cohort 2(683 naive NPC and 303 controls), cfEBV DNA had a sensitivity of 75.84% (AUC = 0.879, 95% CI: 0.86-0.90). There were no significant differences in TNM stage among NPC between the two cohorts (P > 0.05). The MB method considerably increased the positive detection rate of cfEBV DNA in NPCs at stages III-IV, T2-T4, N1-N3, and M0 (P < 0.001). At the end of treatment, 97.51% of patients had no detectable EBV and just 2.49% had detectable cfEBV DNA. Those who received <= 2 or >= 3 cycles of NAC had a median t(1/2) clearance rate of 9.8 days and 12.6 days, respectively. MB based RT-qPCR increased the quantity of cfEBV DNA. MB based RT-qPCR demonstrated superior sensitivity and positive detection rates for cfEBV DNA. cfEBV DNA can be more positively noticed, with a higher diagnostic value and a broader variety of clinical applications among NPC in non-endemic areas.