Compared with the classical strap-down inertial navigation system and the rotating inertial navigation system in being, tri-unit rotating strap-down inertial navigation system has many advantages. Nevertheless, it brings some new problems to data acquisition. In view of the characteristic of this system, such as large amount of data, strong requirement on time synchronization, the impact of time asynchronization both between inertial sensors and between inertial sensors and gratings was analyzed in detail. At the same time, the corresponding solution project was given. In view of the phenomenon that temperature acquisition was disturbed by the rotation of motor easily, the causes were described concretely and relevant measures were taken as well. What’s more, a new communication between digital temperature sensor DS18B20 and DSP was designed in hardware. The result shows the data acquisition instrument comforts anticipative requirements and lay a good foundation for the coming out of high-precision, low-cost inertial navigation system.