For conventional topological phases, the boundary gapless modes are determined by bulk topological invariants. Based on developing an analytic method to solve higher-order boundary modes, we present $PT$-invariant $2$D topological insulators and $3$D topological semimetals that go beyond this bulk-boundary correspondence framework. With unchanged bulk topological invariant, their first-order boundaries undergo transitions separating different phases with second-order-boundary zero-modes. For the $2$D topological insulator, the helical edge modes appear at the transition point for two second-order topological insulator phases with diagonal and off-diagonal corner zero-modes, respectively. Accordingly, for the $3$D topological semimetal, the criticality corresponds to surface helical Fermi arcs of a Dirac semimetal phase. Interestingly, we find that the $3$D system generically belongs to a novel second-order nodal-line semimetal phase, possessing gapped surfaces but a pair of diagonal or off-diagonal hinge Fermi arcs.
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