The invention discloses a tea tree fruit dreg fertilizer and application thereof in improvement of the tobacco leaf squalene content. The tea tree fruit dreg fertilizer is prepared from, by weight, fermented tea tree seed dregs 30-50% and the balance diatomite. The biological and organic tea tree fruit dreg fertilizer improves the tobacco leaf squalene content and the tobacco leaf quality by regulating a soil microenvironment for flue-cured tobacco growth and optimizing a physiological environment for squalene biosynthesis of flue-cured tobacco plants.