To improve the uniformity and controllability of the multifocal array in laser parallel fabrication, a vector iterative optimization phase algorithm is proposed based on the property of the vector Fourier transform in an objective focusing system. Based on this iterative algorithm, a multifocal array with high uniformity can be produced and the position of each focal spot can be precisely controlled. The numerical simulation and experimental results show that the optimized phase can be utilized to generate a multifocal array with high uniformity. Furthermore, applying the homemade femtosecond laser fabrication system based on a spatial light modulator and taking gold films as the sample, we confirm the validity of laser parallel fabrication. The experimental results demonstrate that using the proposed algorithm, one can achieve the laser parallel fabrication based on multifocal array with an arbitrary arrangement structure. In addition, the dynamic scanning laser fabrication can also be realized by dynamically loading phase patterns.