The invention relates to the field of yoghourt processing, in particular to functional yoghourt with long shelf life and a preparation method thereof. The preparation method of the functional yoghourt with long shelf life according to the invention comprises the following steps of: (1) uniformly mixing raw materials, degassing, homogenizing and sterilizing; (2) adding fermentation species, fermenting, filling, and performing post maturation to obtain a finished product; (3) and performing radiation sterilization on the finished product obtained in the step (2) with the radiation dose between 3 kGy and 6 kGy to obtain the functional yoghourt with long shelf life, wherein the fermentation species in the step (2) comprise bifidobacterium infantis. Radiation sterilization is performed with the radiation dose between 3 kGy and 6 kGy, so that the shelf life of the yoghourt can be prolonged; meanwhile, the bifidobacterium infantis is added into the yoghourt, so that the product is endowed with an antitumor function. The yoghourt prepared by using the method has good tissue state, mouthfeel and flavor, does not undergo great changes in the aspects of color, mouthfeel, flavor and tissue within the storage time of six months, and has high stability.