The fossils of Hamipterus tianshanensis (Wang et al. in Curr Biol 24:1323–1330, 2014) and their eggs have important scientific significance because they can provide unique information about the reproduction, development, and evolution of pterosaurs. The fossils and the rock surrounding them have, however, been weathered, which including powdering and flaking, since they were relocated from Xinjiang to Beijing. The high content of soluble salts is a significant factor in fossil deterioration because the dissolution–recrystallization process can generate tremendous pressure and lead to decreased mechanical strength. This study evaluated the electrokinetic desalination performance for the fossils, and two types of poultices employed including paper pulp from Bioline® and CKS121 (cellulose: kaolin: sand = 1:2:1, w/w). Mercury intrusion porosimetry (MIP), scanning electron microscopy (SEM), ion chromatography (IC), and other methods were applied to evaluate the desalination effect. The surface salt content reduction by applied direct current (DC) was about 70%, and the inner salt content reduction was about 80%. The experimental results suggest that the electrokinetic method is a promising way to desalinate fossils. Nonetheless, cracks appeared in the surrounding rock crack after electrokinetic desalination, which can be explained by the montmorillonite swelling-induced stresses. Pre-consolidation, especially for electro-chemical method may solve the cracking problem for the clay-rich sandstone desalination.