The methods for obtaining the solutions to kinematics error with nonparametric constraint and dynamic estimation were proposed herein to estimate the position and orientation of a manipulator in the entire workspace domain. The pose error model of dynamic nonparameterized constraint of manipulator was constructed based on the equivalent differential transformation of the link system, which in turn was based on the error equivalent differential variable and multi-joint motion. This study presented a dynamic functional description of the comprehensive error of the manipulator as the periodic dynamic function related to the joint angle variable was changed. Online decoupling transformation and compensation algorithm of a multi-joint motion space coordinate system were designed in accordance with the coupling law of joint motion of multilink coordinate systems. Verification experiments performed in the entire workspace domain reveal that the error estimation and measured values of the coordinates between the positions have maximum absolute deviations less than 0.01 mm, while the absolute deviation of the orientation angle is less than 0.03°. The experimental results indicate that this method can improve the accuracy and reliability of error estimation in the entire workspace domain.