  We investigate the Glauber divergences in nonfactorizable annihilation
amplitudes for two-body hadronic heavy meson decays in the $k_T$ factorization
theorem at one-loop level. These divergences can be absorbed into the Glauber
factors in the dominant kinematic regions of small parton momenta, which modify
the interference between a nonfactorizable annihilation amplitude and other
amplitudes by rotating it with a phase. We postulate that only the Glauber
effect associated with a pion is significant, due to its special role as a
$q\bar q$ bound state and as a pseudo Nambu-Goldstone boson simultaneously. It
is elaborated that the data of the $D\to\pi\pi$ and $\pi K$ branching ratios
have revealed prominent Glauber effects. This work provides a solid theoretical
ground for the factorization-assisted topological-amplitude parametrization of
two-body hadronic $D$ meson decays.
