The invention discloses an aqueous phase preparation method for a chitosan-quantum dot fluorescent probe, which comprises the following steps of: A, preparing solution of carboxymethyl chitosan: weighing carboxymethyl chitosan, dissolving in a beaker by using double distilled water, and fixing the volume in a bottle for later use; B, preparing solution of CdTe quantum dot: according to the concentration of CdTe quantum dot, transferring the CdTe quantum dot solution to the beaker by using a transfer pipette, adding double distilled water, regulating the pH value to be 7-13, and fixing the volume in a bottle for later use; and C, mixing the prepared carboxymethyl chitosan solution and the CdTe quantum dot solution according to different volume ratios, shaking uniformly and standing at room temperature, or performing ultrasonic wave reaction, oscillating reaction or microwave heating reaction to obtain chitosan-quantum dot fluorescent probes with corresponding luminous wavelengths and different fluorescence intensities. The preparation method has the advantages of simple operation, good water solubility of products, long stabilization time, high yield of fluorescence quantum, good cellular compatibility, and wide application in the aspects of cell and macro-molecular biomarkers.