  We present results from Chandra observations of the cluster lens SDSS
J1029+2623 at z_l=0.58, which is a gravitationally lensed quasar with the
largest known image separation. We clearly detect X-ray emission both from the
lensing cluster and the three lensed quasar images. The cluster has an X-ray
temperature of kT = 8.1 (+2.0, -1.2) keV and bolometric luminosity of L_X =
9.6e44 erg s^-1. Its surface brightness is centered near one of the brightest
cluster galaxies, and it is elongated East-West. We identify a subpeak
North-West of the main peak, which is suggestive of an ongoing merger. Even so,
the X-ray mass inferred from the hydrostatic equilibrium assumption appears to
be consistent with the lensing mass from the Einstein radius of the system. We
find significant absorption in the soft X-ray spectrum of the faintest quasar
image, which can be caused by an intervening material at either the lens or
source redshift. The X-ray flux ratios between the quasar images (after
correcting for absorption) are in reasonable agreement with those at optical
and radio wavelengths, and all the flux ratios are inconsistent with those
predicted by simple mass models. This implies that microlensing effect is not
significant for this system and dark matter substructure is mainly responsible
for the anomalous flux ratios.
