To address the limitations of existing beam alignment approaches in low-power unmanned aerial vehicle (UAV) relay communication systems—which neglect practical deployment configurations of pod-mounted multi-panel phased arrays and fixed-element architectures—an FPGA-based beam alignment implementation framework is proposed. By integrating simulated position and attitude data through coordinate transformations, the methodology introduces dynamically reconfigurable antenna element scales within a multi-panel array coordination architecture. Utilizing beamforming principles to compute angular parameters and phase shift values, the system achieves beam alignment through hardware validation on a field-programmable gate array (FPGA). Simulation results demonstrate that over 70 time slots with a half-beamwidth of 12.7°, the proposed method maintains angular errors below 1°, achieving a power consumption reduction of over 5% compared to conventional algorithms. Notably, the beam alignment latency is measured at 123.4 μs. Hardware validation based on the FPGA platform further confirms the algorithm’s engineering practicality, validating its robustness in real-time UAV relay scenarios.