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In this paper, a new hierarchical software architecture is proposed to improve the safety and reliability of a safety-critical drone system from the perspective of its source code. The proposed architecture uses formal verification methods to ensure that the implementation of each module satisfies its expected design specification, so that it prevents a drone from crashing due to unexpected software failures. This study builds on top of a formally verified operating system kernel, certified kit operating system (CertiKOS). Since device drivers are considered the most important parts affecting the safety of the drone system, we focus mainly on verifying bus drivers such as the serial peripheral interface and the inter-integrated circuit drivers in a drone system using a rigorous formal verification method. Experiments have been carried out to demonstrate the improvement in reliability in case of device anomalies.