It is known that the long time scale fluctuation about 20 times the vortex shedding periodicity exists in the irregularity of the vortex shedding from a two-dimensional circular cylinder. However it's origination is not known yet. Local vortex shedding frequency in spanwise direction is considered to differ from one point to another due to different local Strouhal number caused by flow three-dimensionality. Therefore, interaction between the different vortex shedding frequencies is considered to be the cause of the long time scale fluctuation. In this study, by means of short time Fourier transformation which is modified to have uniform local time response characteristics throughout entire measuring frequency range, modulation characteristics of quasi-instantaneous vortex shedding frequency observed by one point velocity measurement are investigated. Moreover, by means of the modified short time Fourier transformation, two point simultaneous velocity measurements were made to show the existence of the different vortex shedding frequencies at the same time in the spanwise direction.