The invention belongs to the technical field of electric energy quality assessment and particularly relates to a transformer station background harmonic assessment method. The method concretely comprises steps of 1, obtaining monitoring data of an A point if a system is provided with a monitoring point only at an A position, analyzing the data, using different methods for background harmonic assessment according to the load changing condition at the A point, calculating the background harmonic voltages in one month of the A point, averaging the background harmonic voltages and taking the average as the background harmonic voltage during this period, and updating the background harmonic of the A point; and 2, obtaining monitoring data at the monitoring points of A and F if the system is provided with monitoring points at the transformer station A and the important load outlet F, calculating the background harmonic voltage at the monitoring point A, the load at the monitoring point F being an electric railway load, considering intermittence, impact and single phase rectification thereof, and carrying out the background harmonic and negative sequence assessment. The method provides a new thinking for background harmonic calculation when the monitoring data cannot meet requirements of the conventional algorithm.