As the number and geometric intensity of visual satellites are susceptible to large slopes in open-pit mines, we propose integration of GPS/Pseudolites (PLs) positioning technology which can increase the number of visible satellites, strengthen the geometric intensity of satellites and provide a precision solution for slope deformation monitoring. However, the un-modeled systematic errors are still the main limiting factors for high precision baseline solution. In order to eliminate the un-modeled systematic error, the Empirical Mode Decomposition (EMD) theory is employed. The multi-scale decomposition and reconstruction architecture are defined here on the basis of the EMD theory and the systematic error mitigation model is demonstrated as well. A standard of the scale selection for the systematic error elimination is given in terms of the mean of the accumulated standardized modes. Thereafter, the scheme of the GPS/PLs baseline solution based on the EMD is suggested. The simulation and experiment results show that the precision factors (DOP) are reduced greatly when PLs is located suitably. The proposed scheme dramatically improves the reliability of ambiguity resolution and the precision of baseline vector after systematic error being eliminated, and provides an effective model for high precision slope deformation monitoring in open-pit mine.