Recent interests in curvature- and stress-induced pattern formation and pattern selection motivate the present study. Surface morphological wrinkling of a cylindrical shell supported by a soft core subjected to axial compression is investigated based on a nonlinear 3D finite element model. The post-buckling behavior of core-shell cylinders beyond the first bifurcation often leads to complicated responses with surface mode transitions. The proposed finite element framework allows predicting and tracing these bifurcation portraits from a quantitative standpoint. The occurrence and evolution of 3D instability modes including sinusoidally deformed axisymmetric patterns and non-axisymmetric diamond-like modes will be highlighted according to critical dimensionless parameters. Besides, the phase diagram obtained from dimensional analyses and numerical results could be used to guide the design of core-shell cylindrical systems to achieve the desired instability patterns.