Abstract: Focusing on the over-limit unbalance of medium-low voltage (MV-LV) three-phase short-circuit impedance of a 500kV three-phase five-limb site-assembled transformer, this paper traces the root causes from two aspects, including core magnetic boundary difference and millimeter-scale assembly deviation, by combining theoretical analysis, finite element simulation, and field measurement comparison. The research shows that magnetic boundary differences are not the dominant factor in excessive impedance deviations in such transformers; nevertheless, due to the low reference value of MV-LV short-circuit impedance, millimeter-level assembly errors can easily cause the three-phase impedance unbalance to exceed the standard. Optimization suggestions are put forward from the perspectives of process control, on-site assembly constraints, and differentiated acceptance evaluation, which can provide engineering references for impedance precision control and improvement of acceptance criteria of similar site-assembled transformers.