To evaluate the atmospheric effect on low altitude proton variation, we calculated the long-term variation of the lifetimes of low altitude protons which mirror at the geomagnetic equator using empirical models of the atmosphere, the ionosphere, and the geomagnetic field. The calculated results showed that the proton lifetime variation is anti-correlated with the F10.7 solar cycle. The comparison between the estimated and the observed proton fluxes during 20 years showed good agreement at the altitude of the lower drift shell. Our results showed positively that solar cycle variations of the upper atmosphere and the ionosphere had a significant influence on the changes of the low altitude energetic proton flux.