Modern aeronautical Low-Pressure Turbines (LPTs) are prone to aeroelastic instability problems such as flutter. The aerodynamic performance of a modern LPT is often influenced by the interaction between the transient flow and the dynamic behaviour of the blade. Therefore, the investigation and understanding of the physics behind the interaction between the unsteady flow and the flutter phenomenon of the blade in an LPT, which is normally left out by existing studies, is an important aspect of the research to improve the aerodynamic performance of the turbine as well as to ensure the blade mechanical integrity. In this paper, a novel analysis is conducted to explore the flutter instability in a modern LPT, T106A turbine, using two inter blade phase angles (IBPAs), and their effects on the unsteady flow field are investigated. The zero degree and 180 degrees IBPAs are considered in this paper. A high-fidelity direct numerical simulation method is used for the flow simulations. Another distinctive feature of this paper is the use of the 3D model to analyse the effects associated with the 3D blade structure and the 3D vibration mode. The investigation and identification of adequate working ranges of the harmonic balance method, which has been widely used for the aeromechanical analysis of turbomachines, are also presented in this work. This paper will bridge a key gap in the knowledge of aeroelasticity modelling and analysis of modern LPTs.