The invention discloses an embedded controller with an LVDS serial interface and a control method thereof, relates to an embedded controller and a control method thereof, and solves the problem that embedded controllers which are applied to a complex distributed test system are absent at present. The embedded controller comprises an embedded computer, a first FPGA and an LVDS serial interface unit. The control method for the embedded controller comprises that: when a scheduling instruction from other external computers is received, the scheduling instruction is executed; and when a transmitting instruction from an external server is received, data is received through an LAN interface of the embedded computer, and the data is subjected to parallel/serial conversion by the first FPGA and output through the LVDS serial interface unit. The control method for the embedded controller also comprises the regularly receiving process that: monitoring data of each external functional module is regularly acquired through the LVDS serial interface unit, and the data is subjected to the parallel/serial conversion by the first FPGA and transmitted to the embedded computer, and the data is uploaded by the embedded computer through the LAN interface finally. The embedded controller with the LVDS serial interface and the control method thereof are applied to the complex distributed test system.