As the application of optical fiber is boasting, higher quality optical fibers are required in some application fields. Some pinhole defects such as air bubbles, caused during the manufacture of optical fiber, may have severe (or fatal) impacts on precision instruments because of affecting the optical fiber's toughness and signal propagating along the fiber. Therefore, it is very important to detecting the defects in optical fiber using an effective, non-touched, on-line and fast method. A hybrid opto-electronic joint transform correlator (JTC) is competent to do it. The key using the JTC is how to improve discrimination of the detection system. In this paper, through investigating the characteristics of digital joint power spectrum of optical fiber, two data processing methods to improve discrimination of the system are proposed, which are reducing joint-power-spectrum DC item method and binarizing joint power spectrum method. The experimental results show that both methods can greatly increase SNR and reduce the intensity of central peak of the correlation output,and largely improve discrimination probability of the detection system.