The invention discloses a transformer substation three phase linear generalized state estimation method. According to the transformer substation three phase linear generalized state estimation method is used, state estimation is performed in a split-phase and zero-impedance network, and therefore a calculation scale is small, and calculation difficulty is low; three phase multisource real time data from a measuring and control device, a phasor measurement unit and a protection device is used, and therefore data redundancy and calculation reliability of the state estimation are improved; established measurement equations are all linear, calculation does not need iteration, and therefore estimation calculation is simple and rapid; an on and off state pseudo measurement equation is established and used in combination with the measurement equations in the state estimation, bad data identification is performed by using a maximum residual error method, and therefore synchronous identification of analog quantity bad data and topology error is achieved. By using the transformer substation three phase linear generalized state estimation method, the bad data and the topology error are solved in a transformer substation, accurate basic data is provided to a regulation and control center, calculated amount of the state estimation of the regulation and control center is significantly reduced, and reliability is improved.