Provided are a three-dimensional focusing microfluid chip and a manufacturing method thereof. The three-dimensional focusing microfluid chip comprises a dispersed phase layer and a continuous phase layer. The dispersed phase layer comprises a dispersed phase flow channel and a dispersed phase storage pool connected with the dispersed phase flow channel. The continuous phase layer comprises a continuous phase flow channel and a continuous phase storage pool connected with the continuous phase flow channel. A flow channel is formed by the continuous phase flow channel from the continuous phase storage pool, and is divided into two continuous phase flow channel bodies in the middle, the two continuous flow channel bodies are symmetrically distributed on the two sides of the dispersed phase flow channel and intersect and are communicated at an outlet of the dispersed phase flow channel, and a small shrinkage spraying hole is formed. The width dimension of the small shrinkage spraying hole is smaller than the largest width of the intersection of the two continuous phase flow channel bodies. The depth of the continuous phase flow channel is larger than that of the dispersed phase flow channel, an outlet of the dispersed phase flow channel is formed in the middle of the continuous phase flow channel in the depth direction, and a three-dimensional stereoscopic structure is formed. The microfluid chip can effectively generate micrometer-grade and even nanometer-grade tiny droplets through a fluid spraying mode for forming gas covered liquid through gas-liquid two-phase flow.