Humic acids （HAs） with different molecular weights were obtained by ultrafiltration method，and their molecular structures were respectively characterized by FTIR，UV-vis and Fluorescence spectra. A novel electro-Fenton process based on Pd/Fe3O4 nanocatalyst was applied for the effective and simultaneous removal of HAs and Cr（VI）. The results showed that a better mineralization efficiency of HAs was achieved with the increase of their molecular weights，following a descending trend of HA5（87.6%） > HA4（79.0%） > HA3（76.8%） > HA2（70.0%） > HA1（62.9%）. The HAs with high molecular weights was found to exhibit higher removal efficiency，which was attributed to the electrostatic interaction between the negatively charged HAs molecules and the Pd/Fe3O4 nanoparticles. Moreover，the HAs with high molecular weights that possess more conjugated structures and more substituted groups on the benzene rings were readily attacked by the reactive species ·OH，underwent ring-opening reactions till completely mineralized into CO2，whereas the HAs with low molecular weights that have high percentage of carboxylic acids were less active to react with ·OH，resulting in a weak TOC removal efficiency. Meanwhile，the removal of total Cr followed the same decreasing trend of HA5（91.8%） > HA4（88.2%） > HA3（85.9%） > HA2（85.4%） > HA（85.1%），for the HAs with high molecular weights could provide more complexation sites to chromium species，contributing to the removal of Cr（VI） in the developed electrochemical system. In this work，we show that the molecular structures of HAs have effects on the catalytic performance of Pd/Fe3O4 nanoparticles-promoted electrochemical process for the removal of TOC and Cr（VI）.