As a national strategic-level vehicle, a helicopter certainly plays a key role in the nuclear, biological and chemical threat with its ability being capable of rapidly entering and exiting battlefields. To ensure the safety of personnel in cabin, it is necessary to study the NBC protection system of helicopters. In this paper, a helicopter nuclear, biological, and chemical (NBC) protection system is designed in turn from the top-level architecture design of the system based on system integration means. Detailed configuration design is conducted for each sub-system, including air source pressurization sub-system based on a small high speed electric pressurizer, filtration and ventilation sub-system based on the principle of variable pressure adsorption and real-time regeneration on board, temperature control sub-system based on a heat pump-type evaporative refrigeration cycle driven by the use of skidding oil waste heat and parallel drive of double evaporators, and pressure regulation sub-system with integrated cockpit over-pressurization protection and pressurization requirements. Based on the system configuration, a simulation model is established and the dynamic performance of the system is simulated and verified. The simulation results show that under various extreme conditions, both the cabin pressure and the temperature meet the needs of design. While a helicopter enters into the area of NBC threat, the filtration and ventilation subsystem can effectively adsorb toxic substances, and the adsorbent bed is regenerated in real time by on-board, prolonging the operation time in the NBC threat area. The research provides a new idea for the design of helicopter NBC protection system.