To　address　the　slow　scanning　speed　of　the　laser　confocal　method　for　scanning　DNA　chips,　we　designed　and　built　a　CCD　image-based　DNA　chip　scanner.　A　high-powered　LED　was　selected　as　excitation　light　source.　To　avoid　stray　light　in　the　optical　path,　we　designed　a　light　entrance,　an　extinction　dark　room,　a　diaphragm,　and　an　extinctor　that　eliminated　99.95%　of　the　stray　light.　A　focal　automatic　calibration　scheme　is　proposed;　the　only　addition　to　the　hardware　was　the　focusing　motor　and　the　connection　device　between　the　motor　and　the　lens.　Furthermore,　variance　was　used　as　the　image　sharpness　evaluation　function,　with　the　combination　of　rough　and　fine　calibration　to　increase　real-time　performance.　An　experiment　showed　that　the　accuracy　of　automatic　focal　calibration　is　higher　than　that　of　the　manual　method　with repeatability　error　of　2.1%,　and　the　time　required　is　between　18.72　and 55.78　s.　The　sensitivity　can　reach　1.12　flour/µm2　with　a　resolution　of　10.04　µm.　Using　the　proposed　scanner　and　a　commercial　Boao　scanner　on　a　fluorescence　dot　on　the　same　genetic　defect　chip　found　a　consistency　coefficient　of　0.95.　The　scanner　has　the　advantage　of　simple　hardware　structure,　quick　detection,　and　favourite　performance.　©　2019,　©　2019　The　Author(s).　Published　by　Informa　UK　Limited,　trading　as　Taylor　&　Francis　Group.