Diagnosing free electron laser (FEL) polarization is critical for polarization-modulated research such as x-ray FEL diffraction imaging and probing material magnetism. In an electron time-of-flight (eTOF) polarimeter, the flight time and angular distribution of photoelectrons were designed based on x-ray polarimetry for on-site diagnosis. However, the transverse position of x-ray FEL pulses introduces error into the measured photoelectron angular distribution. This work, thus, proposes a method of compensating transverse position jitters for the polarization by the eTOF polarimeter itself without an external x-ray beam-position monitor. A comprehensive numerical model is developed to demonstrate the feasibility of the compensation method, and the results reveal that a spatial resolution of 20 μm and a polarity improved by 0.02 are possible with fully polarized FEL pulses. The impact of FEL pulses and a method to calibrate their linearity are also discussed.