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We investigate photon coalescence in a lossy non-Hermitian system and study a dynamic device modeled by a beam splitter with an extra intrinsic phase term added in the transformation matrix,with which the device is a lossy non-Hermitian linear system.The two-photon interference behavior is altered accordingly since this extra intrinsic phase affects the unitary of transformation and the coalescence of the incoming photons.We calculate the coincidence between two single-photon pulses,considering the interferometric phase between two pulses and the extra intrinsic phase as the tunable parameters.The extra phase turns the famous Hong-Ou-Mandel dip into a bump,with the visibility dependent on both the interferometric phase and the extra phase.