In a multi-modal system which combines thruster and legged locomotion such our state-of-the-art Harpy platform to perform dynamic locomotion. Therefore, it is very important to have a proper estimate of Thruster force. Harpy is a bipedal robot capable of legged-aerial locomotion using its legs and thrusters attached to its main frame. we can characterize thruster force using a thrust stand but it generally does not account for working conditions such as battery voltage. In this study, we present a momentum-based thruster force estimator. One of the key information required to estimate is terrain information. we show estimation results with and without terrain knowledge. In this work, we derive a conjugate momentum thruster force estimator and implement it on a numerical simulator that uses thruster force to perform thruster-assisted walking.