This paper focuses on the kinematic calibration of a modular reconfigurable robot. To aim at low complexity and high generality, a new calibration method was proposed. Based on the definition of independent modules and the kinematics, the kinematic errors were divided into two categories, and will be calibrated respectively. The first category is the individual module errors, which represent the machining errors of modules; they will be calibrated directly by measuring tools. The second category is the assembly errors between consecutive modules, and will be calibrated by using Jacobian. A concept of virtual joint was proposed to deal with the cases that the axes of the errors are not coincident with any rotary joint. The proposed method decouples the errors and lowers the order of calibration equations, and thus has a simple representation and lower computational complexity. The results of the simulation show that the method is of validity, generality, and accuracy.