This paper proposes a novel method to improve the clock bias short-term prediction accuracy of navigation receivers then solve the problem of low positioning accuracy when the satellite signal quality deteriorates. Considering that the clock bias of a navigation receiver is equivalent to a virtual satellite, the predicted value of clock bias is used to assist navigation receivers in positioning. Consequently, a combined prediction method for navigation receiver clock bias based on Empirical Mode Decomposition (EMD) and Back Propagation Neural Network (BPNN) analysis theory is demonstrated. In view of systematic errors and random errors in the clock bias data from navigation receivers, the EMD method is used to decompose the clock bias data; then, the BPNN prediction method is used to establish a high-precision clock bias prediction model; finally, based on the clock bias prediction value, the three-dimensional positioning of the navigation receiver is realized by expanding the observation equation. The experimental results show that the proposed model is suitable for clock bias time series prediction and providing three-dimensional positioning information meets the requirements of navigation application in the harsh environment of only three satellites.