The governing equation, together with the formulas of the averaged flux and the stability parameter for Newtonian fluid flowing in eccentric annulus via the axial reciprocation of the inner tube was established in the bipolar coordinate system. Numerical calculation was conducted for the measurement of water flow using the formulas above, of which the results agree well with the experimental data. It is shown that the flow instability can be induced by the increase of the stroke, the frequency, and the eccentricity of annulus, making the sucker rod more susceptible to partial abrasion. Some protecting methods, including adding centralizers, adjusting the stroke and frequency, are proposed to protect the sucker rod from the partial abrasion, and satisfactory results have been achieved in the oilfields.