Abstract: In this paper, the calibration and uncertainty analysis of the MEMS shear stress sensor are undertaken. Shear stress is generated by the pressure gradient method, the main test equipment is the flat verification water channel. Different voltage outputs are measured under different wall shear stress conditions, and the calibration coefficient can be got through matching the shear stress and voltage with the least square method. The shear stress uncertainty and calibration coefficient uncertainty can be got through measuring the pressure and voltage repeatedly and checking the related product manual. As the result indicated, the uncertainty of the shear stress measurement is within 7%, it tends to be smaller as the free-stream velocity gets higher. The uncertainty of the voltage measurement is within 7%, and it also tends to be smaller as the free-stream velocity gets higher, so that the sensor can be used to wall shear stress measurement reliably. The shape of calibration curve is reasonable, its correlation coefficient of fitting is large enough, it means that the calibration equation is reliably.