The building formation of a one-dimensional nanostructure greatly affects its physical properties. By controlling the supersaturation of deposited molybdenum (Mo) vapor, two kinds of nanostructure building formations can be synthesized in Mo nanocones (spiral- and stacking-type) through a thermal evaporation process. The field emission performances of these two formations are vastly different, particularly with respect to their high current properties. The maximum current of a spiral-type individual Mo nanocone is five times that of the stacking-type nanocone. Electrical transport may not be the decisive factor for this difference because both types of individual Mo nanocones have similar excellent conductivities. Heat conduction during the high current emission process has been considered a primary factor, and it strongly depends on the number of internal nanostructure boundaries in the Mo nanocone. These results indicate that nanostructure building formations with fewer inner boundaries in Mo nanocones contribute to a higher current field emission performance when applied to vacuum electron devices.