The invention provides a data processing method and apparatus, and a computer device. The data processing method comprises the steps of classifying data into security data and non-security data according to transmission paths of the data, wherein the security data and the non-security data are encapsulated with at least one layer of secure communication protocol; encapsulating an internal secure communication protocol for the security data; and transmitting the non-security data and the security data that are encapsulated with the internal secure protocol respectively on different physical channels. Through the invention, the secure transmission of the system data can be guaranteed.