The invention discloses a sequence intercepting method, a device and electronic equipment. The sequence intercepting method comprises the steps of acquiring a reference sequence which is read in a traversal manner and comprises a plurality of paragraphs; acquiring paragraph information and site information of a plurality of to-be-intercepted sequences; according to the traversal sequence of the reference sequence, sequencing the plurality of to-be-intercepted sequences based on the paragraph information and the site information; and in traversal of the reference sequence, successively intercepting the plurality of to-be-intercepted sequences from the reference sequence based on the paragraph information and the site information. Therefore, even aiming at the no-index reference sequence andthe plurality of to-be-intercepted sequences without overlapping and nesting, the plurality of to-be-intercepted sequences can be intercepted in one time through traversal of the reference sequence,thereby remarkably improving interception efficiency.