Precise control of organic molecule deposition on a substrate is quite important for fabricating single-molecule-based devices. In this study, we demonstrate whether a quartz-crystal microbalance (QCM) widely used for a film growth calibration has the ability to precisely measure the number of organic molecules adsorbed on a substrate. The well-known Sauerbrey's equation is extended to formulate the relation between QCM resonant frequency shift and the number of adsorbed molecules onto the QCM surface. The formula is examined by QCM measurements of sublimation of π-conjugated organic molecules and direct counting of the deposited molecules one by one onto metal substrates, using ultrahigh vacuum low-temperature scanning tunneling microscopy (STM). It is revealed that the number of adsorbed molecules evaluated by QCM ( NQCM) show good agreement with those counted from the STM images ( NSTM) within the error of ±25%. The results ensure the QCM capability for controlling the deposition number of organic molecules with high accuracy, that is, if one needs to deposit 100 molecules on the substrate, QCM control promises deposition of 100 ± 25 molecules.