【Objective】 To analyze the difference of circulating threshold (Ct) of polymerase chain reaction (PCR) in blood station laboratories during the external quality assessment, and to put forward suggestions for the quality improvement of participating laboratories. 【Methods】 From 2018 to 2021, the blood station laboratories participated in the external laboratory quality assessment of CITIC including blood screening items with nucleic acid testing method. The data of Roche diagnostic reagent group were used as the source, and the detected Ct values of three groups of quality control samples of HBV A subtype (400 IU/mL), HCV 1b subtype (400 IU/mL) and HIV B genotype (500 IU/mL) were used as the objects. The data were grouped according to quality control (sample) batches, reagent batches and different laboratories. Using the statistical method of variance analysis (assuming P<0.05 as significant), the detected Ct value of each group was analyzed. 【Results】 For the three items (HBV/HCV/HIV), the grouping data involving 42 batches of quality control (13/12/17), 28 batches of reagent (11/8/9) and 57 laboratories (19/19/19) were selected. The grouping analysis of quality assessment batches shows that there was no significant difference between HBV and HCV quality assessment batches, and there was no significant difference between other HIV batches except the two batches of HIV quality assessment samples released in 2021. The grouping analysis of each reagent batch showed that there was no significant difference between each reagent batch for HCV and HIV detection, while there was significant difference between two batches of HBV reagents. After excluding the data groups with significant differences in the quality control batch groups and the reagent batch groups, the detected Ct value of each laboratory group had extremely significant differences in the three items of HBV, HCV and HIV. Through pairing analysis, it was found that four laboratories had significant differences with most other laboratories in the three items, mainly manifested in the high mean value of Ct. 【Conclusion】 For the blood station laboratories with correct test results of quality assessment samples, there are differences in Ct values detected by PCR, which may be mainly caused by the detection ability of the participating laboratories.