This study presents a numerical model of helical gears to consider the effects of shaft and bearing flexibility. A primary feature of this study is that the time-varying mesh stiffness is not just determined by the geometry of gear pair but also updated for each iteration according to the change of center distance. The effects of shaft and bearing flexibilities are discussed by comparing the dynamic response of gear pairs supported with a rigid and a flexible bearing-shaft system. The results show that the pressure angle and contact ratio are significantly changed due to the center-distance variation of gears and the gear pair with a flexible bearing-shaft system has much larger vibration. Finally, experimental tests are conducted to validate the proposed model. The predicted results show good agreement with the experimental data.