Quantum interference effects in the un-modulated quantum systems with light-matter interaction have been widely studied, such as electromagnetically induced transparency (EIT) and Autler-Townes splitting (ATS). However, the similar quantum interference effects in the Floquet systems (i.e., periodically modulated systems), which might cover rich new physics, were rarely studied. In this article, we investigate the quantum interference effects in the Floquet two-and three-level systems analytically and numerically. We show a coherent destruction tunneling effect in a lotuslike multi-peak spectrum with a Floquet two-level system, where the intensity of the probe field is periodically modulated with a square-wave sequence. We demonstrate that the multi-peak split into multiple transparency windows with tunable quantum interference if the Floquet system is asynchronously controlled via a third level. Based on phenomenological analysis with Akaike information criterion, we show that the symmetric central transparency window has a similar mechanism to the traditional ATS or EIT depending on the choice of parameters, additional with an extra degree of freedom to control the quantum interference provided by the modulation period. The other transparent windows are shown to be asymmetric, different from the traditional ATS/EIT windows. These non-trivial quantum interference effects open up a new scope to explore the applications of the Floquet systems.