The invention provides royal jelly and hippophae rhamnoides fruit flavored yogurt and a preparation method thereof. The royal jelly and hippophae rhamnoides fruit flavored yogurt comprises 1-1.5% of royal jelly, 8-10% of hippophae rhamnoides fruit juice, 10-12% of whole milk powder, 6-8% of white granulated sugar, 0.3-0.5% of starch, 0.1-0.3% of lactic acid bacteria powder special for fermentationfor yogurt, and 67.7-74.6% of pure water. The preparation method comprises the following steps of adding the pure water to fresh hippophae rhamnoides fruits, performing pulping in a mashing machine,and after clarifying and filtering, using an edible baking soda solution of which the mass is 0.2% of that of the hippophae rhamnoides fruit juice for regulating the pH of the hippophae rhamnoides fruit juice to be 3.8-4.0 to obtain hippophae rhamnoides fruit juice; and then adding the whole milk powder, the white granulated sugar, the starch and the hippophae rhamnoides fruit juice to the pure water, performing stirring, after fine grinding and homogenizing as well as sterilizing and cooling, adding the royal jelly and a fermenting agent, performing filling and performing fermentation, Finally, the prepared royal jelly and hippophae rhamnoides fruit flavored yogurt is uniform in tissue state, milky in color, unique in flavor, rich in royal jelly and hippophae rhamnoides fruit taste and smell, viscous in mouth feel, moderate in sour and sweet degrees, long in aftertaste, rich in nutrients, simple in preparation technology, and batch production can be performed.