For ultrasonic measurement of bolt axial force, the results are affected by complex correlated multiple factors, which leads to lower measurement accuracy. To measure the axial force of short bolts (M8×37) accurately, theoretical analysis was carried out and a model to estimate measurement error was developed. Several factors in the measurement (such as fluctuation of temperature, position difference of transducer, variation of couplant, etc.) were separated and controlled, and experiments were conducted in two stages to study the influence of multiple factors on the measurement results and to investigate the achievable measurement accuracy. The results show that when bolt axial force is measured by ultrasonic technique, coefficient transforming a time delay of ultrasound waves to the bolt axial force has a significant effect on measurement accuracy, so it should be calibrated precisely and it should be effectively matched with the measured bolt. The fluctuation of temperature and variations of coupling layer reduce the accuracy of measurement results. Hence, temperature compensation and an echo-echo analysis method should be adopted to eliminate the adverse effects from these factors. Inconsistency of transducer position will significantly reduce measurement accuracy; however, abnormal results can be identified and ruled out by correlation analysis. After reasonable and effective process control, measurement accuracy of bolt axial force can be improved, and thus requirements of engineering applications are met.