Put geosynthetic clay liners around underground oil-gas pipelines can reduce the potential damage to environment but it will also affect the distribution of cathodic protection current. Geosynthetic clay liners can be regarded as anisotropic soil structure and the potential distribution on the pipeline between two adjacent cathodic protection stations was calculated based on boundary element method (BEM). The calculation results indicate that potential distribution on the pipeline with geosynthetic clay liner is lower than before. A 1500 m built pipeline with geosynthetic clay liners was selected to be calculated and to perform field test, which shows that the calculation results tally well with the field test results and the validity of the arithmetic in this paper was verified.