The invention provides a non-full-capacity through type cophase power supply device and a control method thereof. The non-full-capacity through type cophase power supply device is composed of a Scotttraction transformer Ttrac and a non-full-capacity cophase power supply converter CP. The electrical isolation of an input side and an output side in the non-full-capacity cophase power supply converter CP is achieved by a high-frequency transformer. An alpha phase and a beta phase of the traction transformer are connected in series to obtain a voltage ualphan1+ubetan2 whose magnitude is a voltageamplitude 1/k (k is greater than 1) of a contact network, the voltage uinv of an output port of the non-full-capacity cophase power supply converter and the above voltage are connected to the contactnetwork in series, and the converter CP only needs to output (1-1/k) of the voltage of the contact network to transmit all active power required by a train. In the case of a difference between the voltages ualphan1+ubetan2 of different power supply stations, the uinv can be adjusted to achieve full-line through type cophase power supply. Meanwhile, the non-full-capacity cophase power supply converter CP can effectively suppress the negative sequence and reactive current of a three-phase grid side by controlling the current iA of a port a and the current iB of a port b.