The invention discloses a reagent supply system for a DNA (deoxyribonucleic acid) sequencer. The reagent supply system comprises a preparing pipeline, a buffer pipeline, a main pipeline, a first multi-pass reversing valve, a second multi-pass reversing valve, a first peristaltic pump for extracting a sequencing reaction reagent and a second peristaltic pump for extracting buffer liquid, wherein the preparing pipeline, the buffer pipeline and the main pipeline are connected through a tee connector, inlets of the first multi-pass reversing valve are respectively communicated with reagent bottles; an outlet of the first multi-pass reversing valve is connected with the preparing pipeline through the first peristaltic pump; an outlet of the second peristaltic pump is connected with the buffer pipeline; an inlet of the second multi-pass reversing valve is connected with the main pipe, and outlets of the second multi-pass reversing valve are respectively communicated with a liquid inlet of areaction cabin and a waste liquor bucket. The invention also discloses a control method of the reagent supply system. According to the reagent supply system disclosed by the invention, the reagent and buffer liquid can be immediately and accurately supplied to a plurality of reaction cabins, so a plurality of reactions are carried out at the same time, a plurality of samples can be sequenced at the same time, and the sequencing efficiency of the DNA is greatly improved.