The invention relates to the field of semiconductor illumination and particularly relates to a wafer-level packaged LED device and a segmentation unit and manufacturing method thereof. The wafer-level packaged LED device includes an LED chip wafer including an LED chip and a phosphor transparent substrate, the phosphor transparent substrate includes a transparent substrate and a phosphor colloid on the transparent substrate, and the surface of the phosphor colloid is combined with the light-existing surface of the LED chip. The wafer-level packaged LED device is segmented into an LED device of a phosphor unit. The wafer-level packaged LED device is manufactured by the combination of wafer-level packaging and an LED chip wafer reversing structure. The obtained LED device improves the light-emitting efficiency, light-existing uniformity and reliability and reduces the blue light edge leakage, and the manufacturing method is efficient and rapid, and the production cost is reduced.