This paper presents new speech analysis method based on a glottal-ARMAX (autoregressive and moving average exogenous) model with phase compensation. A glottal-ARMAX model consists of two kinds of inputs: glottal source model excitation and a white Gaussian input, and a vocal tract ARMAX model. The proposed method can simultaneously estimate the glottal source model and vocal tract ARMAX model parameters pitch synchronously. In this method, ARMAX identification using a modified MIS (model identification system) method is adopted to estimate the ARMAX parameters, and the hybrid approach of the genetic algorithm (GA) and simulated annealing (SA) is employed to efficiently solve the non-linear simultaneous optimization of both parameters. Furthermore, phase compensation using an all-pass filter is introduced within a generation loop in the GA method in order to compensate phase distortion. Experiments using synthetic speech and natural speech demonstrate the efficacy of the proposed method.