The invention discloses a tea tree oil antibacterial microcapsule and a preparation method and application thereof. The method comprises the following steps of mixing a stabilizer and aqueous solution of carboxymethyl chitosan, and stirring the mixture to dissolve the stabilizer to obtain solution I; adding an emulsifier and a grease into the aqueous solution of carboxymethyl chitosan, and homogenizing to obtain solution II; adding the solution II into the solution I, under stirring at the constant temperature of 40 to 60 DEG C, adjusting the pH value of the solution to be between 5.0 to 6.5, and reacting to obtain re-coagulating solution, wherein the using amount of the solution II and the solution I is determined according to the carboxymethyl chitosan, and the proportion by mass of the carboxymethyl chitosan is 1:1.5; and cooling the re-coagulating solution, adjusting the pH value to be between 6.5 to 8.0, adding a curing agent to react and cure to obtain a tea tree oil microcapsule emulsion, and cooling and drying the tea tree oil microcapsule emulsion to obtain the tea tree oil antibacterial microcapsule. The preparation method is simple, the particle size is controllable, and the obtained microcapsule is regular in shape, high in yield and relatively high in packaging rate and medicine loading capacity. When the microcapsule is applied to a water-based formula, the stability is greatly improved.