This paper presents a minimum root-mean-square error (RMSE)-based method for a dual-circle conductance probe array to measure the water holdup of an oil-water two-phase flow in a horizontal oil well. The dual-circle conductance probe array consisting of 24 conductance probes, half of which are equidistantly distributed on a 34 mm radius inner circle and the other half on a 48 mm radius outer circle, is used to estimate the oil-water interface and hence the water holdup in the horizontal oil well. For the same water holdup, the number of probes immersed in water may vary with varying the azimuth angle due to the limited number of probes. The limited number of probes and unknown azimuth angle of the probe array in the oil well limit the measurement accuracy of the water holdup. In order to obtain a better water holdup estimate, a water holdup measurement method based on the minimum RMSE was proposed to decrease the effects of the limited number of probes and unknown azimuth angle of the probe array. To verify the proposed method, numerical simulations were carried out and compared with the commonly used equi-weight estimate method; results showed that the RMSE of the water holdup estimates obtained using the proposed method is smaller than that when using the equi-weight estimate method. Experiments were implemented in a 16 m long and 125 mm inner diameter horizontal pipe on an industrial-scale experimental multiphase flow setup in the Daqing Oil Field, China. The RMSEs of water holdup estimates obtained using the proposed and equi-weight estimate methods are 0.0632 and 0.0690, respectively, showing that the proposed method is better than the equi-weight estimate method.