A main external factor that limits the energy assessment of high-rise buildings in urban areas is the vertical wind conditions. Conventional buildings' energy assessment tools apply a universal vertical wind profile estimation equation in all directions and only consider four typical terrain types. However, the various shape and configurations of buildings in cities can induce the unique wind speed in each direction, and the vertical wind speeds in the same terrain type can be different even in the same city. To get more realistic vertical wind conditions, this study developed an omnidirectional urban vertical wind speed estimation method with direction-dependent building morphologies. A pie-shaped segment method is applied to calculate building morphological features in approaching wind direction. Machine learning methods are developed to calculate parameters of the modified direction-dependent power law urban wind function to convert the Typical Meteorological Year (TMY) wind speed to urban vertical wind speeds. To validate the proposed method, wind tunnel data in Hong Kong are collected for a case study. The results indicate that the proposed method with morphological inputs can effectively estimate the vertical wind speed at different wind directions and heights, and deep neural networks and support vector regression have better performance.