The invention discloses a meteorological satellite data encryption method, which achieves data encryption by adopting an output feedback working mode. Concretely, a ground data transmission subsystem generates an MGK (MESSAGE KEY), and remote-control data input is performed through a ground measurement and control station so as to transmit the MGK to a satellite to participate encryption; and meanwhile, the MGK is encrypted by utilizing an MSK (MASTER KEY) according to a DES (Data Encryption Standard) so as to generate a PBK (PUBLIC KEY), the data transmission subsystem transmits the PBK to a ground receiving station in a ground safe and reliable manner, and a data flow encrypted message is decoded so as to obtain a plaintext. The meteorological satellite data encryption method has the advantages as follows: bit rate and bit error rate are not increased; low probability of break can be achieved, simple encryption and decryption algorithm can be achieved, and hardware equipment is simple and reliable; data can be encrypted in a real-time manner, and a secret key is easy to change; and the switching function between secret transmission and unencrypted transmission can be achieved. The meteorological satellite data encryption method provides references and design considerations to payload data encryption system design of a polar-orbiting meteorological satellite data transmission system.