Second-order topological insulators (SOTIs) are the topological phases of matter in d dimensions that manifest (d-2)-dimensional localized modes at the intersection of the edges. We show that SOTIs can be designed via stacked Chern insulators with opposite chiralities connected by interlayer coupling. To characterize the bulk-corner correspondence, we establish a Jacobian-transformed nested Wilson loop method and an edge theory that are applicable to a wider class of higher-order topological systems. The corresponding topological invariant admits a filling anomaly of the corner modes with fractional charges. The system manifests a fragile topological phase characterized by the absence of a Wannier gap in the Wilson loop spectrum. Furthermore, we argue that the proposed approach can be generalized to multilayers. Our work offers perspectives for exploring and understanding higher-order topological phenomena.