The invention discloses a preparation method of multi-color red beet concentrated juice. The preparation method includes washing, enzyme inactivation by electron beams, crushing, color protection, squeezing, centrifugation, ultrafiltration, concentration, sterilization, aseptic filling and irradiation treatment. The preparation method is simple in technology, has no damage to materials and abandons conventional high temperature enzyme inactivation methods; through the adoption of enzyme inactivation by electron beams, the loss and fading of the materials due to high temperature can be avoided;through electron-beam energy, enzyme inactivation effects can be precisely controlled, browning index can be decreased, and the color and nutrient compositions in red beets can be reserved to a greatextent; and products with multiple colors are prepared through different radiation doses, so that market application scope can be expanded, the demands for multiple colors can be provided, each colorcan be accurately monitored through a color difference meter, and therefore, the uniformity of color difference between finished products can be guaranteed.