We have observed the Class I protostar L1489 IRS with the Atacama Millimeter/submillimeter Array (ALMA) in Band 6. The C$^{18}$O $J=$2-1 line emission shows flattened and non-axisymmetric structures in the same direction as its velocity gradient due to rotation. We discovered that the C$^{18}$O emission shows dips at a radius of ~200-300 au while the 1.3 mm continuum emission extends smoothly up to r~400 au. At the radius of the C$^{18}$O dips, the rotational axis of the outer portion appears to be tilted by ~15 degrees from that of the inner component. Both the inner and outer components with respect to the C$^{18}$O dips exhibit the $r^{-0.5}$ Keplerian rotation profiles until r~600 au. These results not only indicate that a Keplerian disk extends up to ~600 au but also that the disk is warped. We constructed a three dimensional warped disk model rotating at the Keplerian velocity, and demonstrated that the warped disk model reproduces main observed features in the velocity channel maps and the PV diagrams. Such a warped disk system can form by mass accretion from a misaligned envelope. We also discuss a possible disk evolution scenario based on comparisons of disk radii and masses between Class I and Class II sources.