The invention discloses a cooling system of a positron emission tomography scanner. The positron emission tomography scanner comprises a peripheral electronics plate, a detector module and a bottom electronics plate; the cooling system comprises a cooling device, a peripheral cooling air channel, an inner chamber cooling air channel and a bottom cooling air channel; the inner chamber cooling air channel is a chamber body and comprises an air inlet channel and an air return channel; the peripheral electronics plate is located in the peripheral cooling air channel; the detector module is located between the air inlet channel and the air return channel; the bottom electronics plate is located in the bottom cooling air channel; the cooling device is used for conveying cooled air flow to the peripheral cooling air channel, the inner chamber cooling air channel and the bottom cooling air channel so as to cool the peripheral electronics plate, the detector module and the bottom electronics plate. According to the cooling system of the positron emission tomography scanner, ventilation cooling is performed on the peripheral electronics plate and the bottom electronics plate, the low-temperature and stable inner chamber cooling air channel is provided for the detector module, and accordingly the stability and the imaging quality of the system are improved.