A signal separation system is constructed on the multi-pass Thomson scattering system of Heliotron J to solve the problem of overlapping scattered light signals for the electron temperature anisotropy measurement. The phenomenon of overlapping scattered light signals is relieved by operating the signal separation system. A Raman scattering experiment is undertaken to verify the separation effect of the signal separation system. Two scattered light signals corresponding to two adjacent incidences of one laser shot were extended to 104 ns. Moreover, we applied the multi-pass Thomson scattering system with signal separation system to the electron temperature anisotropy measurement. No anisotropy was observed within the error bars in the initial experiment.