The invention discloses a flexible wax oil hydrotreatment process. A wax oil raw material and hydrogen are mixed and then enter a first hydrotreating reactor, and the material passing through an upperhydrotreating catalyst bed layer is divided into two streams; one material stream is extracted out of the first hydrotreating reactor from the middle of the bed layer and mixed with LCO, and the mixture is fed into the second hydrotreating reactor for a hydrogenation reaction; and the other material stream continues flowing downwards through a hydrotreating catalyst bed layer at the lower part; and an obtained first hydrotreating reaction material and an obtained second hydrotreating reaction material are subjected to gas-liquid separation and fractionation to obtain naphtha, diesel oil, hydrogenation heavy fractions and the like. The invention provides the flexible hydrotreatment process for flexibly processing different raw oil and producing high-quality catalytic cracking raw materialson a set of hydrogenation equipment, which can make full use of heat carried by part of a first hydrogenation treatment material and can realize coupling operation of the first hydrotreating reactorand the second hydrotreating reactor.