Dispersion and attenuation estimation of ultrasonic guided waves is important for waveguide characterization. Matrix pencil (MP) method has been proposed for multimode complex wavenumber estimation, but its performance highly depends on the signal to noise ratio (SNR), which still brings challenges for high attenuation waveguide evaluation. In addition, the model order, i.e., matrix size in MP method, significantly impacts the dispersion curve extraction. In this study, to avoid the model order interference and compensate the SNR sensitivity of the classical MP algorithm, a multi-subarrays MP method is proposed for accurate dispersion and attenuation estimation. Considering with different Hankel matrix sizes, the multi-subarrays MP method estimates the complex wavenumbers from each pair of submatrices to filter uncertain results. A soft threshold strategy is applied to compensate the noise sensitivity of the estimation. Simulated results prove the proposed method can improve the dispersion and attenuation curve estimation.