The invention relates to a processing method and system of an electronic confirmation letter based on the Internet. The method comprises the following steps: step S1, receiving a confirmation service request initiated by a letter sending party, electronically signing confirmation letter information, and submitting the confirmation letter information to an authorized party; step S2, after receiving the confirmation letter information by the authorized party, performing sign verification on the confirmation letter information, if the sign verification is passed and authorization confirmation submitted by the authorized party is received, generating a letter of authorization according to the confirmation letter information, electronically signing the letter of authorization, and submitting the signed confirmation letter information and the letter of authorization to a letter reply party; and step S3, performing sign verification on the received confirmation letter information and the letter of authorization by the letter reply party, after the sign verification is passed, adding letter reply information in the received confirmation letter information, generating a letter reply file and signing, uploading the signed letter reply file to a server, and feeding the letter reply file back to the letter sending party. The method and the system provided by the invention can solve the error-prone problem due to complicated work of multiple parties in the confirmation letter service.