The invention provides a momentum wheel friction torque in-orbit real-time estimating method. The method includes the following steps of firstly, collecting and converting momentum wheel parameters; secondly, selecting integral time parameters; thirdly, summating integrals; fourthly, calculating the friction torque. By means of momentum wheel in-orbit real-time rotating speed and momentum wheel drive control voltage torque real-time measurement data, the friction torque in the momentum wheel rotating process can be rapidly estimated, and the precise control over the momentum wheel output torque and the monitoring of the bearing friction torque in-orbit health state are realized.