The present invention discloses an internal protection circuit structure of photovoltaic modules having independent power generating unit, which includes a plurality of solar cells. The plurality of solar cells is combined to form a power generating unit A and a power generating unit B. Polarities of the upper ends of the substrings of solar cell are positive, negative, positive, negative, positive, and negative sequentially from the first column of A to the sixth column of A. Polarities of the lower ends of the substrings of solar cell are positive, negative, positive, negative, positive, and negative sequentially from the first column of B to the sixth column of B. Moreover, the busbar is provided with three separate junction boxes.