A quantum dot ink, a manufacturing method thereof and a quantum dot light emitting diode device are provided. The quantum dot ink includes a non-polar organic solvent, a surface tension modifier and a hydrophobic quantum dot, the quantum dot ink further includes a carrier transport material, wherein phase separation is present between the hydrophobic quantum dot and the carrier transport material. After completing ink-jet printing the quantum dot ink, phase separation occurs between the hydrophobic quantum dot and the carrier transport material. Thus, the two-layer structure of a hydrophobic quantum dot layer and a carrier transport material layer is formed through one process. Not only a quantum dot light emitting device is manufactured by the method of ink-jet printing, but also the operation is simplified, and the manufacturing cost of the quantum dot light emitting device is reduced.