The invention belongs to the dairy product processing field, in particular relating to probiotics yoghurt and a preparation method and application thereof. The invention discloses the probiotics yoghurt which comprises milk; the probiotics yoghurt is characterized in that the probiotics yoghurt also comprises 1.0-10wt% of oligosaccharides and 106-109 cfu/ml of probiotics. The preparation method creatively adopts fermentation by section under different temperatures; the front section ferments under low temperature of 20-40 DEG C; the fermentation under low temperature leads the probiotics to proliferate in large quantity; subsequently, high temperature of 30-50 DEG C is adopted for fermentation so as to lead the probiotics and normal zymogen to quickly ferment together, thus being beneficial for generating good flavor and quality of the product, improving the quality and saving the fermentation time. The probiotics yoghurt has stable probiotics number (more than 106 cfu/g) in the shelf life, has rich milk fragrance, has properly sweet and sour taste, has better taste than general probiotics product, and has the function of improving digestion and enhancing immunity, without side effects.