In this paper, we demonstrate a coincidence counting system with 48 input channels which is aimed to count all coincidence events, up to 531 441 kinds, in a multiphoton experiment. Using the dynamic delay adjusting inside the Field Programmable Gate Array, the alignment of photon signals of 48 channels is achieved. After the alignment, clock phase shifting is used to sample signal pulses. Logic constraints are used to stabilize the pulse width. The coincidence counting data stored in a 1G bit external random access memory will be sent to the computer to analyze the amount of 2-, 3-, 4-, 5-, and 6-fold coincidence events. This system is designed for multiphoton entanglement experiments with multiple degrees of freedom of photons.