The construction project 3^# (gymnasium) building of Core Area Primary School in Tongliang county in Chongqing was taken as the research subject. The vertical vibration modal of long-span prestressed secondary beams floor system was analyzed on simulation. Then the analysis results were compared with the measured results to evaluate the control effect of vertical vibration comfort, and the main conclusions include:the results of the modal analysis of the established accurate finite element model of the long-span floor on the basis of the modeling method are close to the measured results, and the relative error is about 5%. The simulation analysis and engineering measurement show that the first three order vibration modes of long-span floor are dominated by vertical vibration. The fundamental frequency of the structure meets the requirements of the current relevant codes in China, and the vertical vibration comfort conforms to the standard. Compared with the long-span floor which has no bottom plate, the first-order frequency has the smallest increase and it increases by 19.9% after adding bottom plate, which shows that the increase of bottom plate can effectively control the vertical vibration of long-span prestressed secondary beams floor system.