Provided are an anti-sampling offset processing method and apparatus for channel estimation in a wireless communication system, and the method includes: a main path threshold and a first side lobe threshold are acquired based on a result of IFFT during the channel estimation, wherein the first side lobe threshold is smaller than the main path threshold; a noise reduction threshold and a second side lobe threshold are acquired based on a measurement result of Interference on Signal Code Power (ISCP), wherein the second side lobe threshold is smaller than the noise reduction threshold; a predetermined number of strongest paths are selected from main paths determined according to the main path threshold and the noise reduction threshold and a predetermined number of paths adjacent to the strongest paths are labelled as side lobes; and the paths labelled as side lobes are selected according to a final threshold and paths equal to or larger than the final threshold are reserved for participation of subsequent demodulation, wherein the final threshold is the greater one of the first side lobe threshold and the second side lobe threshold. In the present disclosure, impacts of sampling offsets in a wireless communication system on channel estimation are taken into consideration, and side lobes of a main path are introduced into a demodulation process, thereby improving reception performance of a terminal in the wireless communication system.