Restricted Access. Content older than 2 years remains open to all at the journal site(alternative location) ; We present X-ray spectral analysis of five Chandra and XMM-Newton observations of the gravitationally-lensed blazar PKS 1830-211 from 2000 to 2004. We show that the X-ray absorption toward PKS 1830-211 is a variable, and the variable absorption is most likely to be intrinsic with amplitudes of ~2 × 1022–30 × 1022 cm-2 depending on whether or not the absorber is partially covering the X-ray source. Our results confirm the variable absorption observed previously, although interpreted differently, in a sequence of ASCA observations. This large variation in the absorption column density can be interpreted as outflows from the central engine in the polar direction, consistent with recent numerical models of inflow/outflows in active galaxy nuclei. In addition, it could possibly be caused by the interaction between the blazar jet and its environment, or the variation from the geometric configuration of the jet. While the spectra can also be fitted with a variable absorption at the lens redshift, we show that this model is unlikely. We also rule out the simple microlensing interpretation of variability which was previously suggested.