We investigate the stress-driven morphological instability of epitaxially growing multilayer films, which are coherent and dislocation-free. We construct a direct elastic analysis, from which we determine the elastic state of the system recursively in terms of that of the old states of the buried layers. In turn, we use the result for the elastic state to derive the morphological evolution equation of surface profile to first order of perturbations, with the solution explicitly expressed by the growth conditions and material parameters of all the deposited layers. We apply these results to two kinds of multilayer structures. One is the alternating tensile/compressive multilayer structure, for which we determine the effective stability properties, including the effect of varying surface mobility in different layers, its interplay with the global misfit of the multilayer film, and the influence of asymmetric structure of compressive and tensile layers on the system stability. The nature of the asymmetry properties found in stability diagrams is in agreement with experimental observations. The other multilayer structure that we study is one composed of stacked strained/spacer layers. We also calculate the kinetic critical thickness for the onset of morphological instability and obtain its reduction and saturation as number of deposited layers increases, which is consistent with recent experimental results. Compared to the single-layer film growth, the behavior of kinetic critical thickness shows deviations for upper strained layers.