Understanding the aerodynamic hysteresis loop phenomenon is essential when assessing aerodynamic performance and designing aircraft control systems. This phenomenon is a result of time delay effects in unsteady flow. Traditional methods of predicting unsteady aerodynamic forces using computational fluid dynamics have drawbacks, such as long cycles and low efficiency. In this paper, we focus on predicting the aerodynamic hysteresis loop of the NACA (National Advisory Committee for Aeronautics) 0012 airfoil in transonic flow using a new model called LIDNN (Latin hypercube sample input deep neural network). This model integrates input signals and optimization methods to improve upon traditional neural network models. Based on the example validation, the LIDNN model is authenticated as an accurate and efficient method in predicting the unsteady aerodynamic hysteresis loop of the NACA 0012 airfoil in transonic flow, and another significant advantage of the proposed model is its ability to solve multivariable problems effectively, even under varying Mach numbers.