Low-power consumption of orientation estimation using low-cost inertial sensors are crucial for all the applications which are resource constrained critically. This paper presents a novel Lightweight quaternion-based Extended Kalman Filter (LEKF) for orientation estimation for magnetic, angular rate and gravity (MARG) sensors. In this filter, with employing the quaternion kinematic equation as the process model, we derived a simplified measurement model to create the lightweight system model for Kalman filtering, where the measurement model works efficiently and the involved computation of measurement model is reduced. It’s later proved that the proposed filter saves time consumption. Further, due to that no linearization is involved for the proposed measurement model, the good performance would be guaranteed in theory. For the experiments, a commercial sensor for data collection and an optical system to provide reference measurements of orientation, namely Vicon, are utilized to investigate the performance of the proposed filter. Evaluation for different application scenarios are considered, which primarily includes human motion capture and the drone application. Results indicate that the proposed filter provides reliable performance for both applications. What’s more, the comparison experiment shows that the proposed filter provides better performance in terms of either attitude estimation accu- racy or computational time.