The waste neutralization liquor generated during the glyphosate production using glycine-dimethylphosphit process is a severe pollution problem due to its high salinity and organic components. The cement rotary kiln was proposed as a zero discharge strategy of disposal. In this work, the waste liquor was calcinated and the mineralogical phases of residue were characterized by scanning electron microscope (SEM) and X-ray diffraction (XRD). The mineralogical phases and the strength of cement clinker were characterized to evaluate the influence to the products. The burnability of cement raw meal added with waste liquor and the calorific value of waste liquor were tested to evaluate the influence to the thermal state of the kiln system. The results showed that after the addition of this liquor, the differences of the main phases and the strength of cement clinker were negligible, the burnability of raw meal was improved; and the calorific value of this liquor was 6140J/g, which made it could be considered as an alternative fuel during the actual production.