A high-stability dual-frequency laser source is a key technology for achieving national ultra-precision measurement capability and also the foundation for supporting the quality of high-end equipment manufacturing. In this work, a high-stability dual-frequency laser source and its frequency difference stability evaluation system are both built based on a double acousto-optic modulation scheme. By investigating the mechanism of generating dual-frequency laser based on double acousto-optic modulation, a degradation model of frequency difference stability is constructed, and targeted technical improvements are implemented. The study shows that the frequency stability of the dual-frequency laser source and the stability of the frequency difference both affect the accuracy of heterodyne interference measurement. The frequency difference stability is determined by factors such as the stability of RF signal and the nonlinear distortion of the power amplifier. This study first optimizes the frequency difference stability to 7.5×10^–10@1 s and 1.2×10^–9@1000 s by designing a high-order harmonic filtering technique. Then, the DG 4202 RF generator is replaced with a rubidium-clock-based high-stability RF signal generator, thus further optimizing the frequency difference stability to 9×10^–11@1 s and 6×10^–10@1000 s. The influence of dual-frequency frequency difference stability on heterodyne interference measurement accuracy is reduced to the sub-femtometer level. And the frequency difference stability of the dual-frequency laser source fully meets the application requirements of picometer-level laser interference measurement. Combined with the most advanced frequency stabilization technology using ultra-stable cavity, our high-stability dual-frequency laser source can support heterodyne interference measurement with picometer or even femtometer-level accuracy, demonstrating significant potential for applications in fields such as ultra-precision measurements.