The integrated modular avionics (IMA) architecture is an open standard in avionics industry, in which the number of functionalities implemented by software is greater than ever before. In the IMA architecture, the reliability of the avionics system is highly affected by the software applications. In order to enhance the fault tolerance feature with regard to software application failures, many industrial standards propose a layered health monitoring/fault management (HM/FM) scheme to periodically check the health status of software application processes and recover the malfunctioning software process whenever an error is located. In this paper, we make an analytical study of the HM/FM system for avionics application software. We use the stochastic Petri nets (SPN) to build a formal model of each component and present a method to combine the components together to form a complete system model with respect to three interlayer query strategies. We further investigate the effectiveness of these strategies in an illustrative system. The integrated modular avionics (IMA) architecture is an open standard in avionics industry, in which the number of functionalities implemented by software is greater than ever before. In the IMA architecture, the reliability of the avionics system is highly affected by the software applications. In order to enhance the fault tolerance feature with regard to software application failures, many industrial standards propose a layered health monitoring / fault management (HM / FM) scheme to periodically check the health status of software application processes and recover the malfunctioning software process whenever an error this located. In this paper, we make an analytical study of the HM / FM system for avionics application software. We use the stochastic Petri nets (SPN) to build a formal model of each component and present a method to combine the components together to form a complete system model with respect to three interlayer query strategies these strategies in an illustrative system.