Objective To explore the differences between ABI 7500 and TL 988 fluorescent quantitative instrument for polymerase chain reaction. Methods Based on EP9-A2 Files, quantitative influenza A virus positive controls of five kinds of concentrations were detected by two kinds of fluorescence quantitative PCR instruments at the same time, and each sample was detected 20 times. The precision and sensitivity between the two kinds of instruments were compared. Results Inner group CV of TL 988 ranged from 0.68% to 1.52%. The CV for ABI 7500 ranged from 1.93% to 2.69%. The high (107, 106, 105 copies/mL) levels of IFVA positive control were detected by ABI 7500 and TL 988 instruments, and there were no significant difference between the results(P>0.05) while the low(104, 103 copies /mL)levels were de-tected by ABI 7500 and TL 988 instruments, and there was a significant difference between the results(P<0.05). When samples were detected at the level of 103 copies/mL, the positive detection rate was 100% with TL 988 instrument, but the positive detection rate was 0 with ABI 7500 instrument. The related index of ABI 7500 and TL 988 was better (r=0.998). Conclusion The performances in precision and sensitivity of TL 988 PCR instrument are better than ABI 7500 PCR.