The wetting process and the wetting state transition stages are studied on hydrophilic rough surfaces covered with microscale pillar arrays of different geometrical morphologies and distributions. The effects of geometrical morphology, distribution, parameters, hydrophilicity, and contact angle hysteresis of pillar arrays on wetting state transition are analyzed by an energy method. The results indicate that on the hydrophilic rough surface covered with hexagonal arrays of square pillars, the water droplet tends to stay in a stable Cassie state, or the wetting state transits only from a Cassie state to an intermediate state. Moreover, smaller pillar interval, larger square pillar width or diameter of cylinder, higher pillar height, strong hydrophilicity are beneficial to the stability of Cassie state, therefore, the wetting state could be prevented from transforming to pseudo-Wenzel state or Wenzel state. However, smaller area fraction of solid-liquid interface under the water drop and weaker hydrophilicity is beneficial to increasing the apparent contact angle. Therefore, the stability of wetting state and the large apparent contact angle should be considered in hydrophilic surface design. The contact angle hysteresis gives rise to an opposite effect on wetting state stability and the hydrophobicity or superhydrophobicity of rough solid surface. The results provide a theoretical foundation for designing the substrates covered with hydrophilic rough structures, on which the water droplet will obtain a stable Cassie state.