The invention relates to a system for rapidly, directly, absolutely and quantitatively detecting microbes based on a liquid drop by using a liquid drop micro-fluidic technology, and a method thereof. The system comprises a micro-fluidic chip, a plurality of cell collecting, culturing and observing chambers, an optical detection unit and an image processing unit. The method comprises the following steps: preprocessing a sample, injecting the preprocessed sample into the micro-fluidic chip to form monodispersed unicellular liquid drops, and carrying out controlled temperature cell culture on the monodispersed unicellular liquid drops formed in the cell collecting, culturing and observing chambers for 1-2h; and determining the existence of living cells and the growth speed of the cells according to the turbidity of a single liquid drop, collecting the amplified pictures of the liquid drops in the cell collecting, culturing and observing chambers, and counting the turbid liquid drops to obtain the quantity of the microbes in the sample. The system for rapidly, directly, absolutely and quantitatively detecting microbes based on a liquid drop and the method have the advantages of simplicity and low cost, are suitable for portable onsite detection and laboratory detection, and can be used to detect microbe indexes in the fields of foods, environment, drugs sanitation products and cosmetics.