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A total of 26 strains of lactic acid bacteria were screened with the aim of achieving a high flavonoid aglycone conversion rate in fermented seabuckthorn juice. The fermentation was optimized through single strain selection, followed by mixed inoculation. Lactobacillus plantarum L23, Pediococcus pentosaceus P27, and Lactobacillus plantarum L21 emerged as the most efficient conversion strains used for mixed inoculation. Subsequently, the orthogonal test was conducted to optimize pH value, temperature, and carbon source addition. The flavonoid aglycone content (calculated by isorhamnetin) was measured as a primer value for optimization. After screening, the highest flavonoid aglycone content was obtained under the following conditions: pH value of 4, temperature of 30 °, carbon source of 6% (m/V), and inoculation ratio of 1:2:1. The contents of total flavonoids, total phenolic acid, organic acid, and crude polysaccharides were measured before and after fermentation of seabuckthorn raw juice. The flavonoid aglycone content increased by approximately 90%, whereas the total flavonoid content increased by approximately 108%. In this formula, the contents of crude polysaccharide, organic acid, and total phenolic acid were also significantly different from those of the original seabuckthorn juice before fermentation. This study serves as a valuable reference for investigating the conversion mechanism of flavonoid aglycones using lactic acid bacteria, providing guidance for further industrial processing of seabuckthorn in China. [ABSTRACT FROM AUTHOR]