The invention discloses a water soluble metal selenide nanoparticle and a preparation method and application thereof in a lithium ion battery negative electrode material, and belongs to the technical field of the lithium ion battery negative electrode material; and the method is as follows: evenly stirring cuprous chloride, stannic chloride, oleylamine and oleic acid at room temperature, quickly injecting a diphenyl diselenide oleylamine solution at 220-230 DEG C into the mixture for reacting at 235-250 DEG C for 5 to 30 minutes, and naturally cooling to room the temperature to obtain oil soluble metal selenide nanocrystals; mixing ethanol and 3-mercaptopropionic acid, evenly stirring at the room temperature, then adjusting the pH of the reaction solution to 10-11; under room temperature conditions, adding acetone into an ultrasound reaction liquid and oil soluble metal selenide nanocrystal toluene solution mixture for centrifugation, precipitating, washing, and drying under vacuum to obtain the water soluble metal selenide nanoparticle with the particle size of about 20-30 nanometers. The method has the advantages of simple preparation process and good process reproducibility, and the product has the advantages of stable structure, good conductivity, high charge and discharge specific capacity, high rate, stable cycling charge and discharge, and the like.