Monopulse is a classical technique for radar angle estimation and still adopted for fast angle estimation in phased array antenna. The classical formula can be applied to a 2-dimentional phased array antenna if two conditions—the unbiasedness and the independence of the azimuth and the elevation estimate—are satisfied. However, if the sum and difference beams are adapted to suppress the interference under jamming condition, they can be severely distorted. Thus the difference beams become highly correlated and violate the conditions. In this paper, we show the numerical implementation of the generalized monopulse estimation using the distorted and correlated beams, especially for a subarray configured antenna. Because we use the data from the measured subarray patterns rather than the mathematical model, this numerical method can be easily implemented for the complex array configuration and gives good performance for the uncertainty of the real system.