This paper analyzes the philosophical foundation of individualized cultivation of innovative talents in top universities under the guidance of Marx's"Individuality Development Theory", in view of the great task of "construction of top universities and top disciplines " put forward by the state. In other words, human’s personality can be recognized and changed, it can also achieve a breakthrough and development under the dual shape of self and society. Top universities should transform enthusiasm of college students into self-development power through a seriesof adjustments in institutional mechanisms. The paper also proposes several approaches to the individualized cultivation of innovative talents in top universities, such as simplifying the concept of individualized cultivation of innovative talents, adjusting the way of individualized cultivation of innovative talents, improving the system of individualized cultivation of innovative talents and developing the function of implicit education in the individualized cultivation of innovative talents.