One major systematic error for free-fall atom gravimeters is the effect of two-photon light shift (LS2). In the process of evaluating LS2, the results can be affected by the residual frequency error of direct digital synthesizers due to necessary experimental parameter changes. In this paper, the impact of the coupling effect between the frequency error and LS2 has been investigated and analyzed, along with the related physical mechanisms. The parameters of the frequency error sequence, such as the time step of δt and the time delay of Δt, significantly affect the bias and uncertainty of LS2. Notably, when these parameters are significantly altered or misaligned, the impact can reach several tens of µGal. Conversely, when they remain within the optimal ranges, the impact can be minimal. Specifically, when δt is less than or equal to 10 µs, the impact on the LS2 bias is less than 0.3 µGal, with the contribution to the total uncertainty of the gravity value being approximately 0.1 µGal. Furthermore, after correcting the phase shift introduced by the frequency error, the evaluation results have a similar improvement effect on the whole. Compared to the LS2 theoretical value, the residual is generally on the order of µGal. Through the comprehensive analysis and optimization, as well as related experiments, this cross-effect is managed and decoupled, leading to accurate LS2 evaluation results. This improvement ensures a better accuracy in the obtained absolute gravity values. The analysis methods discussed can provide an effective strategy for enhancing the performance of atom gravimeters.