The present invention provides a certificate loading method and a certificate updating method of a card reader and the card reader. The certificate loading method comprises: verifying whether a signature of a first certificate to be loaded is legitimate according to a public key of an application root certificate in the card reader; If the signature is legitimate, analyzing the first certificate, to obtain a public key of the first certificate; encrypting preset data by using the public key, to obtain encrypted data after encryption; decrypting the encrypted data according to a private key of a pre-generated public-private key pair, to obtain data after decryption, wherein the private key is a private key corresponding to the public key of the first certificate in the public-private key pair that is pre-generated by the card reader and is used to acquire the first certificate; and determining whether the data after decryption is consistent with the preset data, if yes, writing the first certificate to a specific location of the card reader, to finish loading of the first certificate. According to the method, after a safety certificate is loaded into the card reader, legality, confidentiality and integrity of information can be ensured in a transaction process with a CPU card.