The ultra-thin vapor chamber (UTVC) technology offers an attractive approach for thermal management of micro devices due to tiny volume, flat contact area and high temperature uniformity. In this paper, a 3D transient numerical model of UTVC is established to study the performance of the UTVC. The numerical method takes into account the variation of saturation pressure with saturation temperature. The Marangoni effect on the evaporation process is also discussed in wick microstructure. The modified boundary conditions are proposed to couple Marangoni effect on the liquid flow and pressure drop. According to the modified numerical method, the transient characteristics of UTVC are analyzed. The numerical results have excellent agreement with the experimental results and the maximum relative error is less than 1%. The numerical analysis result shows that the UTVC has rapid transient thermal response time and the time for UTVC to reach the steady state was less than 60 s at three heat loads. The pressure drop of UTVC is mainly in the vapor region, but the pressure drop of liquid increases by 12% after considering Marangoni effect. Comparing different copper column models, the increase of rows can increase the overall pressure drop of UTVC; but it can also improve the temperature uniformity of heating area and slightly reduce the overall thermal resistance before capillary limit is reached. The shape of copper column has little effect on the thermal performance of UTVC, while the influence of pressure drop is circular < diamond < square. These results provide valuable suggestions in design of copper columns to decrease pressure drop and improve thermal performance of UTVC.