Directed self-assembly of polymers on chemically homogeneous and heterogeneous patterns is of considerable interest for nanolithography and nanofluidic devices. By employing dissipative particle dynamics (DPD) technology, we explore the nanoscale phase separation of comb-like block copolymers (CBCPs) confined at chemically homogeneous and heterogeneous substrates. Herein, the geometric and energetic influences of striped substrates on the microphases are firstly studied using various geometries of annular stripes for the heterogeneous substrates. Different parameters including the stripe geometry, substrate selectivity, and film thickness are studied systematically. T-Junction lamellae and acclivitous alignment are achieved on the heterogeneous substrates because of the synergy of geometrical effects of the striped pattern from heterogeneous substrates together with weak preference of the substrates toward one of the CBCP components. In this study, we provide a detailed understanding of microphase separation of CBCPs on the heterogeneous substrates, and the approach outlined in the present study offers a crucial tool for experimentalists to design CBCP thin films with complex device-oriented structures.