Wingtip-joined modular High-Altitude Long-Endurance (HALE) Unmanned Aerial Vehicles (UAVs), or multi-body aircraft (MBA), promise enhanced endurance but face gust-induced instability challenges due to unique aeroelastic dynamics. This study characterizes MBA gust response and evaluates active control for gust load alleviation (GLA). An aeroelastic model is used in time-domain simulations of single, dual, and triple-module configurations under discrete gusts, investigating the impact of module number and inter-module flexibility. A PID controller, applied per module in a dual-module setup, is assessed for GLA. Results show modular assembly significantly alters gust response via modified stiffness and new compound motion modes. The PID controller achieved a 38.4% maximum peak acceleration reduction. This work advances understanding of MBA gust behavior and demonstrates active PID control’s significant potential for enhancing their operational stability against discrete gust encounters.