To meet the demand of joint torque measurement for a modular reconfigurable robot, a harmonic drive built-in torque measuring method was proposed. The robot and its joint module and the torque measuring principle were first introduced. Based on the two-order ripple model, strains on the flexspline were then analyzed. A new measuing method based on double compensations was proposed. This method cancels out the first order ripples by individual channels, and then cancels out the remain ripples by weighted stacking the signals. The relationship between output signal and torque was given, and a new gain-tuning method was presented. Finally, a simulation was conducted. The simulation proves that the proposed torque measuring method is correct and of high accuracy.