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Rheumatoid arthritis (RA) is a chronic autoimmune disease that primarily affects peripheral synovial joints, like fingers, wrist and feet. Radiology plays a critical role in the diagnosis and monitoring of RA. Limited by the current spatial resolution of radiographic imaging, joint space narrowing (JSN) progression of RA with the same reason above can be less than one pixel per year with universal spatial resolution. Insensitive monitoring of JSN can hinder the radiologist/rheumatologist from making a proper and timely clinical judgment. In this paper, we propose a novel and sensitive method that we call partial image phase-only correlation which aims to automatically quantify JSN progression in the early stages of RA. The majority of the current literature utilizes the mean error, root-mean-square deviation and standard deviation to report the accuracy at pixel level. Our work measures JSN progression between a baseline and its follow-up finger joint images by using the phase spectrum in the frequency domain. Using this study, the mean error can be reduced to 0.0130mm when applied to phantom radiographs with ground truth, and 0.0519mm standard deviation for clinical radiography. With its sub-pixel accuracy far beyond manual measurement, we are optimistic that our work is promising for automatically quantifying JSN progression.