Type Iax supernovae (SNe Iax) are an important subluminous class of SNe Ia. However, their progenitors and explosion mechanisms are not yet understood. It has been suggested that SNe Iax may be produced from weak deflagration explosions of Chandrasekhar-mass white dwarfs (WDs) in binary systems with a helium (He) star donor. In such progenitor systems, the stripped He companion material caused by the ejecta-companion interaction is expected to present some He features in their late-time spectra. However, the detection of He lines in late-time spectra of SNe Iax has not yet been successful, which gives an upper limit on the amount of stripped He mass of . In this work, we study the interaction between SN Iax ejecta and a He star companion by performing three-dimensional hydrodynamical simulations with a weak pure deflagration explosion model. We find that about of He material can be stripped off from the companion star by SN explosion, which is very close to (or lower than) the observational upper limit on the total stripped He mass in SNe Iax. We, therefore, conclude that nondetection of He lines in late-time spectra of SNe Iax could be reasonably explained if they indeed resulted from weak pure deflagration explosions of Chandrasekhar-mass WDs in progenitor systems with a He star donor.