Current orbit uncertainty propagation (OUP) and orbit determination (OD) methods suffer from drawbacks related to high computational burden, limiting their applications in deep space missions. To this end, this paper proposes a multivariate attention-based method for efficient OUP and OD of Earth–Jupiter transfer. First, a neural network-based OD framework is utilized, in which the orbit propagation process in a traditional unscented transform (UT) and unscented Kalman filter (UKF) is replaced by the neural network. Then, the sample structure of training the neural network for the Earth–Jupiter transfer is discussed and designed. In addition, a method for efficiently generating a large number of samples for the Earth–Jupiter transfer is presented. Next, a multivariate attention-based neural network (MANN) is designed for orbit propagation, which shows better capacity in terms of accuracy and generalization than the deep neural network. Finally, the proposed method is successfully applied to solve the OD problem in an Earth–Jupiter transfer. Simulations show that the proposed method can obtain a similar estimation to the UKF while saving more than 90% of the computational cost.