A method and apparatus for pulse interference suppression, and a computer readable storage medium in a communication system are provided in the embodiments of the present invention. The method includes: judging a location where pulse interference occurs according to a power of a signal; and performing suppression processing on a data segment interfered by a pulse in the location. After judging that the pulse interference exists in the location, a receiver in the communication system discards the data segment interfered by the pulse in the location, and feeds back an indication that the data are not received.