We theoretically demonstrate quantum interference in an anti-parity-time (anti-PT) symmetric system based on coupled waveguides. We calculate the coincidence probability in an input polarization-entangled two-photon state, which can be used to simulate different statistical particles. When the birefringence of the waveguides is negligible, our results indicate that the coincidence probabilities of the bosons and fermions decrease exponentially with the propagation distance in both the unbroken and broken anti-PT symmetry regions owing to the dissipation. Particularly, loss-induced transparency is observed for the bosons. Simultaneously, the statistical rule valid in the Hermitian system is violated and the antibunching of bosons is observed. When the birefringence of the waveguides is considered, the coincidence probability of the bosons and fermions is equalized at the exceptional point (EP), whereas that of the bosons is less(greater) than that of the fermions in the broken(unbroken) anti-PT symmetry region. Additionally, we observe the Hong-Ou-Mandel dip for bosons in the broken anti-PT phase. Our research provides a complementary technique for the manipulation of quantum interference compared with the PT symmetric system and may be applied in building quantum devices with anti-PT symmetric quantum mechanics.