The present invention discloses a watermelon juice probiotic fermented beverage and a preparation method thereof. The beverage preparation method uses watermelons as raw materials, scientifically blends prebiotic factors, does not add any essences and coloring matters, mainly uses low-temperature processing technology such as ultrasonic wave cleaning, high-pressure pulsed electric field treatment, biological enzymolysis, vacuum degassing, etc. in the whole process, replaces the existing heat sterilization and enzyme blunting technology, maintains the color and luster, flavor and mouth feel of the natural watermelon juice to a maximum degree, enhances the non-biological stability and biological stability of the watermelon juice, reduces the addition of chemical additives, increases the juice squeezing rate and food safety of the watermelon juice, and has a probiotic live bacteria content of 7 multiplied by 10^11 to 8 multiplied by 10^11 cfu/ml. The watermelon juice probiotic fermented beverage is environmentally friendly, can be processed into probiotic solid beverage and quantitatively packaged beverage which have natural taste, are nutritious and health-care, are convenient to drink, and have longer shelf lives, opens up a new way for watermelon deep processing and industrial development, and can achieve better economic and social benefits.