We carry out three-dimensional hydrodynamic simulations of the supernova remnants (SNRs) produced inside molecular clouds (MCs) near their surface using the HLL code (Harten et al. 1983). We explore the dynamical evolution and the X-ray morphology of SNRs after breaking through the MC surface for ranges of the explosion depths below the surface and the density ratios of the clouds to the intercloud media (ICM). We find that if an SNR breaks out through an MC surface in its Sedov stage, the outermost dense shell of the remnant is divided into several layers. The divided layers are subject to the Rayleigh-Taylor instability and fragmented. On the other hand, if an SNR breaks through an MC after the remnant enters the snowplow phase, the radiative shell is not divided to layers. We also compare the predictions of previous analytic solutions for the expansion of SNRs in stratified media with our one- dimensional simulations. Moreover, we produce synthetic X-ray surface brightness in order to research the center-bright X-ray morphology shown in thermal composite SNRs. In the late stages, a breakout SNR shows the center-bright X-ray morphology inside an MC in our results. We apply our model to the observational results of the X-ray morphology of the thermal composite SNR 3C 391.