This paper deals with the Noether’s theory for variable mass system on time scales. The calculus on time scales unifies and extends variable mass system continuous model and discrete model into a single theory. Firstly, Hamilton’s principle of the variable mass system on time scales is given. Secondly, based on the quasi-invariance of the Hamilton’s action under a group of infinitesimal transformations, Noether’s theorem and its inverse theorem of the variable mass system on time scales are presented. Finally, two examples are given to illustrate the applications of the results.