An organic thin film transistor, a manufacturing method thereof and an array substrate are provided. The manufacturing method of an organic thin film transistor includes: forming an organic semiconductor layer; partially sheltering the organic semiconductor layer, so that a sheltered region and an unsheltered region are formed on the organic semiconductor layer, the sheltered region corresponding to a region where an active layer of the organic thin film transistor needs to be formed; and doping the organic semiconductor layer, so that the organic semiconductor layer in correspondence with the sheltered region is not doped, and the organic semiconductor layer in correspondence with the unsheltered region is doped.