The invention provides a method for efficiently and quickly determining the BAC (
bacterial artificial chromosome) terminal sequence. The method comprises the following steps: (1) with a super
cell as a unit, enriching all BAC terminal sequences in the row cells, column cells and plate cells in each super
cell to obtain a
library suitable for a new-generation sequencing platform; (2) sequencing on the new-generation sequencing platform; and (3) regressing the mixed BAC terminal sequences to single
cloning through the method of
bioinformatics: determining the information of the row
cell, column cell and plate cell of each BAC terminal sequence through
sequence comparison, and positioning the BAC terminal sequence of each
cloning. The method provided by the invention not only can quickly obtain the BAC terminal sequences of all single
cloning in the whole BAC
library, but also reduces the cost and time of BAC terminal sequencing to a great degree.