This paper aims to enhance the signal separation accuracy of phase-sensitive optical timedomain reflectometry (Φ-OTDR) under thermo-mechanical coupling (TMC). For this purpose, the Φ-OTDR signal was firstly separated by genetic algorithm-empirical mode decompositionnonnegative matrix factorization (GA-EMD-NMF). Then, the Kalman-proportional-integralderivative (PID) method was introduced to further separate the data. Taking the TMC as the input, a feedback model was constructed by the genetic algorithm-radial basis function (GA-RBF) to decouple the TMC. To tackle the 3D Φ-OTDR data, a 3D speeded up robust features (SURF) method was developed to reconstruct the box filter and Gaussian pyramid based on the features of the 3D data, thereby enhancing the positioning accuracy of Φ-OTDR signal. Later, several experiments were carried out in a semi-anechoic room, which proved that the proposed method outperforms the traditional methods. The research findings shed new light on signal separation of Φ-OTDR.