To meet the demand of thermal management with large power and high heat flux in the future engineering applications, more and more attentions have been draw to develop the two-phase microchannel cooling technology. In this work, a three dimensional numerical investigation is performed to study the influence of mass flux and heat flux on the two phase flow boiling characteristics in a single microchannel with large length-to-diameter ratio. The related calculation results show that the Volume of Fluid (VOF) model coupled with Lee model can predict the two phase pressure drop and heat transfer coefficient of the microchannel well. And the flow patterns in the microchannel are classified as bubbly flow, slug flow and annular flow, which can be captured by this numerical model precisely. Besides, the transient pressure drop augments with the increase of mass flux. But the effect of mass flux on the amplitude of quasi-steady pressure drop and the peak value of time-averaged heat transfer coefficient along the microchannel is small. At last, the amplitude of quasi-steady pressure drop increases with the augmentation of heat flux. The maximum and fully developed time-averaged heat transfer coefficients along the microchannel increase with the heat flux.