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The strange timing property of X-ray pulsar 1E 1207.4-5209 can be explained by the hypothesis that it is a member of an ultra-compact binary system. This paper confronts the ultra-compact assumption with the observed properties of this pulsar. The gravitational potential well of an ultra-compact binary can enlarge the corotation radius and thus make it possible for accreting material to reach the surface of the NS in the low accretion rate case. Thus the generation of the absorption features should be similar to the case of accreting pulsars. The close equality of the energy loss by fast cooling of the postsupernova neutron star and the energy dissipation needed for a wide binary evolving to an ultra-compact binary demonstrates that the ultra-compact binary may be formed in 10-100yr after the second supernova explosion. Moreover, the ultra-compact binary hypothesis can well explain the the absence of optical counterpart and the observed two black body emissions. We suggest a simple method which can test the binary nature directly with XMM-Newton and Chandra observations. We further predict that the temperature of the two black bodies should vary at different pulse periods.