We study the phase transition phenomenon inherent in the shuffled (permuted) regression problem, which has found numerous applications in databases, privacy, data analysis, etc. In this study, we aim to precisely identify the locations of the phase transition points by leveraging techniques from message passing (MP). In our analysis, we first transform the permutation recovery problem into a probabilistic graphical model. We then leverage the analytical tools rooted in the message passing (MP) algorithm and derive an equation to track the convergence of the MP algorithm. By linking this equation to the branching random walk process, we are able to characterize the impact of the signal-to-noise-ratio ($\snr$) on the permutation recovery. Depending on whether the signal is given or not, we separately investigate the oracle case and the non-oracle case. The bottleneck in identifying the phase transition regimes lies in deriving closed-form formulas for the corresponding critical points, but only in rare scenarios can one obtain such precise expressions. To tackle this technical challenge, this study proposes the Gaussian approximation method, which allows us to obtain the closed-form formulas in almost all scenarios. In the oracle case, our method can fairly accurately predict the phase transition $\snr$. In the non-oracle case, our algorithm can predict the maximum allowed number of permuted rows and uncover its dependency on the sample number.