For the aeroengines, thrust is a crucial performance parameter which is closely related to the mission accessibility. Accurate thrust control is conducive to excavate the potential of the variable cycle engine (VCE) in different operation modes, which meets the requirements of future engine control system. However, the thrust is unmeasured in flight. Besides, the traditional thrust estimation method is difficult to meet the wide-area thrust control requirements due to the strong nonlinearity and large flight envelope for a neoconfiguration VCE of the high-flow triple-bypass, named high-flow dual variable cycle engine (HDVCE). This paper proposes a novel online fusion thrust estimation method mainly under single operation mode for the HDVCE. The problem of individual engine differences is also focused, and the combination of model and data-driven is to generate the thrust estimation with fusion strategy. At first, a multi-combustion chamber coupled dynamic model is established for the HDVCE, and an adaptive network is used for model optimization to improve the model accuracy. On this basis, an EKF-based thrust estimator is built. Secondly, a data-driven thrust estimator is pre-trained by a stacked autoencoder (SAE) and then tuned by back propagation (BP) neural network. Subsequently, the thrust integration is incorporated based on estimation results from the EKF-based and data-driven one using Euclidean distance fusion strategy. Simulation results show that the fusion estimation method proposed in this paper, on the one hand, reduces the effect of model instability on EKF. On the other hand, it ensures the estimation accuracy of SAE-BP far from the training point. The comparisons also reveal that the fusion one produces more than 97% in thrust estimation accuracy and is better than the remaining ones, which is promising for thrust control applications.