The invention discloses a method based on PCI-E interface full algorithm cryptographic card, including: a cryptographic algorithm module, a FLASH memory, a PCI-E bus interface, a random numb generator, and an FPGA master control chip with NIOS soft core processor, wherein a PCI-E IP core and an algorithm state machine are integrated in the FPGA master control chip. The cryptographic algorithm module comprises a symmetric key encryption SM4 algorithm chip, a symmetric key encryption SM1 algorithm chip and an asymmetric key encryption SM2 algorithm chip. The invention also discloses an encryption method of the cipher card. The invention provides a high-performance full-algorithm cryptographic card, which simultaneously reduces the complexity of hardware circuit and energy consumption, improves the key operation speed, and the cryptographic card adopts a home-made cryptographic algorithm, so that the user's key is most securely protected.