The invention relates to a method for detecting somatic cell mutation of paraffin section samples based on next-generation sequencing and a device thereof in the field of next-generation sequencing analysis. The method comprises the following steps: obtaining a filter parameter as a filter threshold when the somatic cell mutation of a fresh tumor frozen tissue sample and the somatic cell mutationof a tumor tissue paraffin section sample have the highest consistency; detecting somatic cell mutation of the tumor tissue paraffin section sample to be detected; filtering out sites that coincide with the mutation site set of normal samples; filtering out somatic cell mutation sites that do not reach the filter threshold; and filtering germ cell mutation and high frequency mutation sites. By using PON, the specific somatic cell mutation site filter threshold based on paraffin section tissue characteristics and the germ cell mutation and high frequency mutation sites filtered with the existing database as filtering conditions for the somatic cell mutation detection, most false positive results caused by paraffin section preparation can be quickly eliminated, detection efficiency and specificity can be improved, and somatic cell mutation of paraffin sections can be quickly and accurately detected.