Thermoacoustic instability in a reacting flow field is characterized by high amplitude pressure fluctuations driven by a positive coupling between the unsteady heat release rate and the acoustic field of the combustor. In a turbulent flow, the transition of a thermoacoustic system from a state of chaos to periodic oscillations occurs via a state of intermittency. During the transition to periodic oscillations, the unsteady heat release rate synchronizes with the acoustic pressure fluctuations. Thermoacoustic systems are traditionally modeled by coupling the model for the heat source and the acoustic subsystem, each estimated independently. The response of the unsteady heat source, i.e., the flame, to acoustic fluctuations is characterized by introducing unsteady external forcing. The forced response of the flame need not be the same in the presence of an acoustic field due to their nonlinear coupling. Instead of characterizing individual subsystems, we introduce a neural ordinary differential equation (neural ODE) framework to model the thermoacoustic system as a whole. The neural ODE model for the thermoacoustic system uses time series of the heat release rate and the pressure fluctuations, measured simultaneously without introducing any external perturbations, to model their coupled interaction. Furthermore, we use the parameters of neural ODE to define an anomaly measure that represents the proximity of system dynamics to limit cycle oscillations and thus provide an early warning signal for the onset of thermoacoustic instability. © 2022 Author(s).