We discuss level splitting and sideband transitions induced by a modulated coupling between a superconducting quantum circuit and a nanomechanical resonator. First, we show how to achieve an unconventional time-dependent longitudinal coupling between a flux (transmon) qubit and the resonator. Considering a sinusoidal modulation of the coupling strength, we find that a first-order sideband transition can be split into two. Moreover, under the driving of a red-detuned field, we discuss the optical response of the qubit for a resonant probe field. We show that level splitting induced by modulating this longitudinal coupling can enable two-color electromagnetically induced transparency (EIT), in addition to single-color EIT. In contrast to standard predictions of two-color EIT in atomic systems, we apply here only a single drive (control) field. The monochromatic modulation of the coupling strength is equivalent to employing two eigenfrequency-tunable mechanical resonators. Both drive-probe detuning for single-color EIT and the distance between transparent windows for two-color EIT, can be adjusted by tuning the modulation frequency of the coupling.