A series of new AIE systems based on the pyrimidothienopyrimidine skeleton were efficiently synthesized and fully characterized. These compounds exhibited weak emission in solution but strong solid-state fluorescence with a red shift. Notably, compound 16 displayed unique white-light emission from a single-component system and tunable emission colors in DMF/water mixtures. This dual emission behavior, arising from AIE and excimer formation, is unprecedented for pyrimidothienopyrimidine derivatives. Although compounds 9a and 9b exhibited AIEE behavior, compounds 15c and 18 demonstrated AIE behavior, with significantly enhanced fluorescence intensity upon water addition. Moreover, most synthesized compounds exhibited moderate to strong antimicrobial activity against various bacterial and fungal strains, suggesting their potential for biological applications.