The invention provides an IQ independent processing method for a satellite high-speed digital transmission system. The method comprises: separating a received data frame into two baseband signals I and Q, wherein the data frame comprises a data sequence and an auxiliary sequence at the frame header; determining the output position of the auxiliary sequence according to the correlation peak positions of the components of the two baseband signals I and Q and a standard auxiliary sequence in the I and Q; and constructing first plural auxiliary sequences of the I and Q according to two adjacent real symbols of the output auxiliary sequence; and performing frequency offset estimation on the baseband signals I and Q according to the constructed first plural auxiliary sequence. The invention alsoprovides an IQ independent processing device for a satellite high-speed digital transmission system. The IQ independent processing method and device are satisfy the need for a very-high speed systemfor independently sampling I and Q, significantly reduce hardware requirements and transmission overhead and maintain system performance loss within an acceptable range.