The invention provides an FPGA-based flexibly configurable power grid data monitoring and processing system and method. The system comprises a data acquisition module and a data analysis module. Wherein the data acquisition module and the data analysis module are interconnected through a backboard PCIe X8 bus; The data acquisition module comprises an analog quantity acquisition unit, a switching value acquisition unit, a GOOSE message acquisition unit and an acquisition FPGA. And the data analysis module comprises a data processing FPGA, an optical port, an Ethernet port, an SATA hard disk, aDDR4 memory and a synchronous clock generation unit. According to the invention, the FPGA is used as a core device for power grid data processing; Data acquisition, data processing and data communication are all completed by the FPGA, which is different from the traditional FPGA + DSP + ARM architecture, the advantages of the FPGA in the aspects of algorithm acceleration calculation and programmable logic are fully exerted, and the power consumption, the flexibility degree, the integration level and the calculation capability are improved.