Modern avionics systems are complex safety-critical cyber-physical systems (CPSs). Failure probabilities allocation is the important work for civil airborne systems and equipment during the preliminary system safety assessment process. Architecture analysis and design language (AADL) is suitable for the design and development of avionics systems. It is indispensable to perform failure probabilities allocation and safety assessment for AADL models. This study proposes an AADL-based failure probabilities allocation approach, which considers the design of system architectures, model complexities and severity levels. It allocates failure probabilities to subcomponents as safety requirements. Furthermore, with the integration of the proposed allocation approach and deterministic stochastic Petri-net (DSPN), an AADL-based safety assessment method is proposed. It transforms AADL models to DSPN models to calculate failure probabilities of subcomponents and assesses if subcomponents can satisfy safety requirements, so that an architecture that satisfies safety objectives can be obtained. Finally, the algorithm and the structure of the tool are provided for failure probabilities allocation and safety assessment approaches. By assessing flight control systems, it is demonstrated that proposed approaches can effectively perform failure probabilities allocation and safety assessment.