In this study, Fe/N/S co-doped biochar was prepared from coffee grounds for using as particle electrodes (PE) to construct a three-dimensional electrochemical system (3DES). Tetracycline (TC) was selected as the simulated contaminant to evaluate the performance of 3DES in removing trace organic contaminates form water. First, characteristics analysis revealed that the PE was the micron-level carbon-based solid material with good electric conductivity, excellent catalytic performance and stability. Then, the performance of the 3DES was evaluated. About 92% of TC and 76% of total organic carbon (TOC) was removed under optimal operation conditions of potassium peroxydisulfate (PDS) addition of 3mM, current density of 100mA·cm−2, PE dosage of 0.5g·L−1 and solution initial pH of 7. The 3DES exhibited satisfactory stability and application prospect for trace organic contaminates treatment in real water. Furthermore, analysis of the reactive oxidized species (ROS) revealed that the 1O2 and O2•− contributed much more to the TC removal than •OH and SO4•−. In addition, three possible pathways of TC removal in 3EDS was proposed. TC was degraded to organics with simple structures through functional group removal, ring-opening, and C=O bond rupturing, and finally mineralized into CO2, H2O, and NO3-, etc. Finally, toxicity evaluation of the intermediate products indicated that the ecological risks of TC was effectively reduced through 3DES. This study provided a new strategy for resource utilization of carbon-based solid waste and efficient treatment of refractory wastewater.