During the working of portable flexible CMM, the mechanical arm’s gravity and operating load generate dynamic strain, the thermal distortion also results in its length change. The caused errors would severely deteriorate the measuring accuracy. An error compensating system of the mechanical arm is designed in this paper, based on the monitor of dynamic strain and environmental temperature. The mathematical model of portable flexible coordinate measuring machine (CMM) was established.For the dynamic strain, four resistance strain gauges are sticked symmetrically on the root of each mechanical arm to monitor the dynamic strain. Then length error caused by the measuring arm’s gravity or external operation load can be calculated through the analysis of stress. Strain compensation can be realized, when they are fed back to the measurement procedures. For thermal distortion, the temperature values acquired by the single-linear digital thermometer are substituted in the correction formula to calculate the relevant compensation dosage. Finally, these compensation dosages are feedbacked to the measuring program to have these errors compensated continually. The integrated error compensation system can improve the measurement accuracy of portable flexible CMM effectively.