Three-dimensional radar combined with an automatic dependent surveillance-broadcast (ADS-B) device is a typical multisensor data-fusion system. To estimate the system error of three-dimensional radar, a least-squares-based radar system error method (FL-LSr) using ADS-B measurements is proposed in a local rectangular radar coordinate system. In the proposed method, a unified observed model is established first, and the radar measurements and ADS-B measurements are transformed into the unified coordinated system. Then, the outliers in radar measurements are eliminated according to the 3σ rule. The corresponding sampling time of radar measurements is regarded as the reference time, and interpolation from straight-line fitting is used to reconstruct the ADS-B measurements. Additionally, the radar measurements and ADS-B are fitted to two straight-lines, and the angle between these two straight-lines is applied to compensate the azimuth components of radar measurements. Finally, the least squares estimation algorithm is utilized to estimate the system error of the three-dimensional radar. Experimental results with real data illustrate that the proposed method can estimate radar system error effectively and accurately compared with traditional radar system error estimation methods.