  Gamma-ray binary systems, a subclass of high-mass X-ray binaries, show
non-thermal emissions from radio to TeV. While efficient electron acceleration
is considered to take place in them, the nature of the acceleration mechanism
and the physical environments in these systems have been a long-standing
question. In this work, we report on long-term recurrent patterns in the
short-term variability of the soft X-ray emission of LS 5039, one of the
brightest gamma-ray binary systems. The Neutron star Interior Composition
Explorer (NICER) observed LS 5039 four times from 2018 to 2021. By comparing
them with the previous Suzaku and NuSTAR long-exposure observations, we studied
the long-term evolution of the orbital light curve in the soft X-ray band.
Although the observations by NICER and Suzaku are separated by $\sim$14 years,
i.e., more than 10^3 orbits, the orbital light curves show remarkable
consistency after calculating their running averages with a window width 70 ks.
Furthermore, all of the light curves show short-term variability with a time
scale of $\sim$10 ks. Since the column density did not vary when the flux
changed abruptly, such a short-term variability seems to be an intrinsic
feature of the X-ray emission. We propose that the short-term variability is
caused by clumps (or inhomogeneities) of the companion star wind impacting the
X-ray production site. The observed time scale matches well with the lifetime
of the clumps interacting with the pulsar wind and the dynamical time scale of
the relativistic intrabinary shock in the pulsar wind scenario.
