While sub-continuum heat conduction becomes more important as the size of micro/nanodevices keeps shrinking under the mean free path of heat carriers, its computation still remains challenging to the general engineering community due to the lack of easily accessible numerical simulation tools. To address this challenge, this article reports the finite element analysis (FEA) of transient ballistic-diffusive phonon heat transport in a two-dimensional domain using a commercial package (COMSOL Multiphysics). The Boltzmann transport equation under the gray relaxation-time approximation was numerically solved by discretizing the angular domain with the discrete ordinate method (DOM) and the spatial domain with the FEA. The DOM-FEA method was validated by comparing the results with different benchmark studies, such as the equation of phonon radiative transfer, the ballistic-diffusive equation, and the finite difference method of the phonon Boltzmann transport equation. The calculation of phonon heat transport for a 2-D square slab reveals that heat conduction becomes more ballistic with temperature jumps at boundaries as Knudsen number (Kn) increases. The ballistic nature also significantly affects transient thermal behaviors at high Kn numbers. The obtained results clearly demonstrate the capability of the DOM-FEA as a promising engineering tool for calculating sub-continuum phonon heat transport. (C) 2014 Elsevier Ltd. All rights reserved.