A method for measuring the residual phase noise(RPN) of long microwave optical links(MOLs)and individual components in the MOL was proposed in this paper. Compared with the previous RPN measurement methods, the two-tone correlation-based method suppressed the noise contributions of the uncorrelated noise sources except that of the device under test(DUT). By this method, the RPN of externally modulated long MOLs was measured, the RPN of a 6 km MOL was successfully measured to be -130 dBc/Hz at 1 kHz offset and -140 dBc/Hz at 10 kHz offset, compared with a 1 m short MOL, the RPN deteriorated about 10 dB. In addition, in order to find out the relationship between the RPN and the RF power compression due to the nonlinearity of the photo-electric detector (PD), the RPNs of the PD with different incident optical powers and bias voltages were also measured by this method. The experimental results reveal that the nonlinearity of PD can deteriorate its RPN.