The measuring mechanism of the self-aligned interferometer (SI) is analyzed in detail in the paper. The expression of nonlinear phase shift and its error expression are derived. The reasons of influencing on the measuring accuracy of the nonlinear phase shift are analyzed theoretically. The influences of the SI structure parameters on measuring the nonlinear phase shift are simulated and calculated. Properly selecting structure parameters in the SI, the optimal value and are obtained. A measuring system using the optimal structure parameters is set up. The measured nonlinear phase shift coincides with the theoretical value. When compared the measured with other testing values from reference , the deviation obtained in our experiment is smaller. The experimental results show that the measuring method with simulating and optimizing the structure parameters in the SI is effective and convenient. The measuring method improved will be applied widely in optical fiber communications and optical precise measurements.