In this paper, an advanced fruit fly algorithm (FOA) is proposed and applied in subarray phased array antenna synthesis. The proposed algorithm introduces orthogonal crossover, quantum selection and simulated annealing operations on the individuals, and then combines them by using an adaptive expansion-contraction factor. Accordingly, a linear generation mechanism of candidate solution based fruit fly algorithm (LGMS-FOA) is generated, in which individuals are selected in a highly balanced way, and the poor solutions are still accepted with a varying probability during the iteration. These mechanisms help the proposed algorithm enhance the population diversity and global searching capability but avoid falling into local optimum. Numerical classical unimodel benchmark functions are provided to test the proposed algorithm (OLFOA) in comparison with other advanced algorithms. In addition, to further validate its superiority, the proposed algorithm is applied to handle the subarray array synthesis of several tough planar and circular apertures with different array sizes and subarray shapes. Simulation results show that the proposed OLFOA can achieve better performance than other improved evolutionary algorithms.