We present the spectral modulation of an optofluidic microdisk device and investigate the mechanism and characteristics of the microdisk laser in aqueous media. The optofluidic microdisk device combines a solid-state dye-doped polymer microdisk with a microfluidic channel device, whose optical field can interact with the aqueous media. Interesting phenomena, such as mode splitting and single-mode lasing in the laser spectrum, can be observed in two coupled microdisks under the pump laser. We modulated the spectra by changing the gap of the two coupled microdisks, the refractive indices of the aqueous media, and the position of a pump light, namely, selective pumping schemes. This optofluidic microlaser provides a method to modulate the laser spectra precisely and flexibly, which will help to further understand spectral properties of coupled microcavity laser systems and develop potential applications in photobiology and photomedicine.