The invention discloses a self diagnosis system based on channels of an FPGA analog input device. The self diagnosis system is connected with an analog input device and comprises an FPGA processing unit, an acquisition AD channel, a self diagnosis DA channel and an isolation cell; the FPGA processing unit is connected with the acquisition AD channel and the self diagnosis DA channel, the acquisition AD channel comprises an analog switch, an A/D converter and an isolation unit which are sequentially connected; and the self diagnosis DA channel comprises a D/A converter and an isolation unit. The invention also discloses one self diagnosis method of the self diagnosis system based on the channel of the FPGA analog input device, self diagnosis of a 16-channel analog quantity acquisition channel is realized in parallel, and time cost is reduced. Reliability is high, full-channel and full-code-value parallel detection is realized, and all the channels of the input device do not acquire an external signal on site when self diagnosis operation is carried out. Electrical security is high, and data processing function and the channels of the input device realize electric isolation.