The irradiation of femtosecond light pulses onto nano-objects creates localised optical fields on the nanostructure surfaces. Plasmonic effects spatially modulate the local-field distribution, achieving optical control of an ultrafast electron source on a scale of approximately 10 nm. Further miniaturisation of such an electron source down to an atomistically small scale is technically difficult by modulating the local-field distribution via plasmonic effects. Here, by illuminating recently identified single-molecule electron sources with femtosecond light pulses, we discovered that largely modulated emission patterns appeared from single C60 molecules, approximately one nanometre in size. Our simulations revealed that the emission patterns represented the single-molecule molecular orbitals (MOs), and the observed modulations originated from the variations of the single-molecule MOs, practically achieving subnanometric optical modulation of an electron source. Our work has thus demonstrated a simple way to continue miniaturising the spatially-controlled electron source down to an atomistic scale using quantum effects.