Abstract: An automatic nucleic acid detection system and a method thereof are disclosed. The automatic nucleic acid detection method includes: performing, by an automatic control subsystem, on a nucleic acid extraction machine platform, a nucleic acid extraction on one or more specimens in a sample tray to generate one or more corresponding nucleic acids in the sample tray; distributing, by the automatic control subsystem, on a nucleic acid distribution machine platform, the nucleic acid in each hole of the sample tray and a first reagent into a plurality of holes of a detection tray, wherein the number of holes of the detection tray is greater than that of the sample tray; and performing, by the automatic control subsystem, on a nucleic acid detection machine platform, a nucleic acid detection on the detection tray.