Field-emitted, low-energy electrons from the conducting tip of an atomic force microscope were adopted for nanolithography on calixarene ultrathin films coated on silicon wafers. A structural evolution from protrusion to depression down to a 30 nm spatial resolution was reproducibly obtained by tuning the sample voltage and exposure current in the lithography process. Close analyses of the profiles showed that the nanostructures formed by a single exposure with a high current are almost identical to those created by cumulative exposure with a lower current but an equal number of injected electrons. Surface potential imaging by Kelvin probe force microscopy found a negatively charged region surrounding the groove structures once the structures were formed. We conclude that the mechanism related to the formation of a temporary negative state and molecule decomposition, rather than thermal ablation, is responsible for the low-energy field-emission electron lithography on a calixarene molecular resist. We hope that our elucidation of the underlying mechanism is helpful for molecular resist design and further improving the reproducibility and throughput of nanolithography.