The main purpose of this paper is to develop an automatic print head alignment algorithm for a material jetting-based color 3D additive manufacturing system. This printing system has six print heads, respectively, filled with six different photocurable resin (C, M, Y, K, W) and support. Start of all, the printing system with initial parameters prints a standard platform, which is used to confirm whether the print head is aligned well or not. Next, a scanner is used to gain the printed image. An image processing algorithm is used to get the characteristic points of the capture image and calculate the compensation parameters, which will be imported to the printing system and make the system aligned well. This paper proposed an automatic smart print head alignment algorithm, which can be used on multiple print head based- 3D additive manufacturing system. Replacing of human alignment, this technology can save more time and reduce the error. It also can automatically work and oversee the system in real-time, which will improve the quality and the color performance of the printed products.