Micro-thermometer is an important tool to measure the refractive index structure constant. The rapid change of atmospheric temperature is the measuring object, so accurate and effective signal collection of temperature fluctuation is the precondition of demarcating micro-thermometer successfully. In view of two-channel wind tunnel micro-thermometer calibrating system, the multiple-channel data acquisition program is programed based on PCI-1002 acquisition card. With the combination of high-precision timer of Windows operation system and MFC programming frame, the accurate and efficient multiple-channel acquisition to temperature fluctuation signal is performed, and the data sets are displayed, stored and computed in computer systems at the same time. The results show that by using high-precision timer of Windows system, the data gathering program works properly and can provide a reliable support for micro-thermometer experiment.