The modulated wideband converter (MWC) is a sub-Nyquist sampling system recently proposed for sampling sparse multi-band signals. However, due to non-ideal analogue components, transfer-matrix calibration is required for the successful reconstruction. In practice, it is difficult to control the phases of the consecutive sinusoidal inputs precisely which are used to calibrate the transfer-matrix. Here, the authors propose a method of transfer-matrix calibration for the MWC with digital expanded channels when the phases of the sinusoidal inputs are unknown. As the oblique elements of the MWC transfer-matrix are equal, the authors can estimate the unknown phases first. The authors then obtain the actual transfer-matrix by phase correction. Finally, the validity of this method is verified by simulation and hardware experiment. The system performance is measured by computing the signal-to-noise ratio and the mean-square error between the original and reconstructed signals.