A manufacturing method of a vertical channel transistor array is provided. The method includes following steps. A plurality of embedded word lines are formed at bottoms of trenches, and each of the embedded word lines is located at a first side wall of one of the trenches and connected to first sides of the semiconductor pillars in the same row. Each of the embedded word lines is not connected to second sides of the semiconductor pillars in the same row, and the first sides are opposite to the second sides. Only one embedded word line is correspondingly connected to the semiconductor pillars arranged in one row. An isolation structure is formed between a second side wall of each of the trenches and each of the embedded word lines. The first side wall is opposite to the second side wall.