MEMS-based skin friction sensors are used to measure and validate skin friction and its distribution, and their advantages of small volume, high reliability, and low cost make them very important for vehicle design. Aiming at addressing the accuracy problem of skin friction measurements induced by existing errors of sensor fabrication and assembly, a novel fabrication technology based on visual alignment is presented. Sensor optimization, precise fabrication of key parts, micro-assembly based on visual alignment, prototype fabrication, static calibration and validation in a hypersonic wind tunnel are implemented. The fabrication and assembly precision of the sensor prototypes achieve the desired effect. The results indicate that the sensor prototypes have the characteristics of fast response, good stability and zero-return; the measurement ranges are 0–100 Pa, the resolution is 0.1 Pa, the repeatability accuracy and linearity are better than 1%, the repeatability accuracy in laminar flow conditions is better than 2% and it is almost 3% in turbulent flow conditions. The deviations between the measured skin friction coefficients and numerical solutions are almost 10% under turbulent flow conditions; whereas the deviations between the measured skin friction coefficients and the analytical values are large (even more than 100%) under laminar flow conditions. The error resources of direct skin friction measurement and their influence rules are systematically analyzed.