The stacking configuration of two-dimensional materials critically governs their optical and electronic responses. Monolayer transition-metal dichalcogenides (TMDC) lack inversion symmetry and exhibit exciton-enhanced second-harmonic generation (SHG). In TMDC bilayers, near-60° (H- or AB-stacked) and near-0° (R- or AA-stacked) alignments are conventionally associated with suppressed and enhanced SHG, respectively, owing to destructive or constructive interference between the layer-resolved nonlinear polarizations. Here, combining atomic-resolution multislice electron ptychography, stacking-sensitive exciton-hybridization spectroscopy, energy- and phase-resolved SHG measurements, and excitonic first-principles calculations, we establish the opposite correspondence in MoTe2/WSe2 heterobilayers: the nearly AA-stacked configuration exhibits destructive SHG, whereas the nearly AB-stacked configuration exhibits constructive SHG. This reassignment resolves the apparent inconsistency between the previously reported quantum anomalous Hall phenomenology and the theoretically expected stacking dependence of topological moiré bands. We show that the reversed SHG interference originates from distinct two-photon resonances associated with the WSe2 C exciton and the MoTe2 D exciton, which generate a nearly π relative phase between the layer-resolved second-order nonlinear susceptibilities near the commonly used ∼800-nm excitation. In small-angle twisted MoTe2/WSe2, the interplay between this relative phase and the twist angle continuously controls the SHG polarization state. When Δϕ + 3α = 180°, the output approaches circular polarization (ellipticity  0.91) and undergoes an abrupt 90° azimuthal rotation, corresponding to a geometric polarization singularity on the Poincaré sphere. Our results establish a calibrated stacking–SHG correspondence for MoTe2/WSe2 and highlight the need for phase-aware stacking identification in resonantly excited TMDC heterobilayers.