A method for investigating transformer substation watt hour meter secondary return circuit faults via use of bus unbalance rates and belongs to the field of detection. The method comprises the following steps: statistics are run on watt hour meter secondary return circuit fault types according to actual operation data of a transformer substation. For watt hour meters of two wire connection modes including a three-phase four-wire system and a three-phase three-wire system, coefficients of correlations between watt hour meter display electric quantities following all kinds of faults and watt hour meter display electric quantities in normal operation conditions are respectively derived, prognosis of faults can be realized based on watt hour meter fault analysis results and electric quantity data of bus balance report forms, and possible fault lists and possible fault types can be found prior to on-site troubleshooting operation. Via a technical solution of the method disclosed in the invention, a relation between the display electric quantities following the different kinds of faults and the normal electric quantities can be visually reflected, direct prognosis of possible faults can be realized according to monitoring data, and on-site troubleshooting operation can be conducted conveniently; the method is characterized by accuracy, reliability, wide application scope and the like; the method can be widely applied to the field of identification and elimination of the transformer substation watt hour meter secondary return circuit faults.