To develop efficient photoactive agents with satisfactory fluorescence, photodynamic, and photothermal effects is crucial for a phototherapeutic strategy to combat cancer diseases and pathogenic microbes. Herein, a water-soluble donor−acceptor−donor (D−A−D) structured conjugated oligomer was designed and synthesized, consisting of two cyclopenta-dithiophene (CDT) units as the electron donor and boron dipyrromethene (BODIPY) as the electron acceptor. Upon excitation, dual emission was observed for CDT-BODIPY with blue and red fluorescence peaks at 463 nm and at 730 nm, respectively, which was ascribed to intramolecular charge transfer (ICT). Due to the ICT effect, the singlet-to-triplet intersystem crossing rate of CDT-BODIPY was also enhanced, leading to an outstanding photodynamic behavior to produce reactive oxygen species (ROS). Meanwhile, its low bandgap also enabled it a moderate photothermal capability with a conversion efficiency of 33.1%. Taking advantage of its phototriggered activities, this conjugated oligomer exhibited an effective inhibition behavior on the pathogenic growth of Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Candida albicans (C. albicans), which can be guided by dual-wavelength fluorescence imaging. This D−A−D type conjugated oligomer with balanced photophysical characteristics provides a promising strategy to imaging-guided photoactive therapy.