Two analogs of thionaphthoquinone dyes, viz; AMT; 2-((thiophen-2-yl)methylamino)-3-chloro-naphthalene-1,4-dione and AET; 2-((thiophen-2-yl)ethylamino)-3-chloro-naphthalene-1,4-dione are synthesized from 2,3-dichloronaphthalene-1,4-dione and were used as light harvester in the TiO2 and ZnO based dye-sensitized solar cells (DSSC's). FT-IR analysis of AMT and AET showed N-H band’s existence at 3316 cm-1 and 3269 cm-1, respectively. X-Ray Crystallographic Data Collection and Refinement confirms the AMT crystallizes in monoclinic space group P2/c. The optical properties of the photosensitizers loaded ZnO shows the broadband in the UV region assigned to π → π⃰ transition while a visible region band assigned to n → π⃰ charge transfer transition. The photovoltaic performances of thionaphthoquinone photosensitizers in TiO2 nanorod and ZnO nanograin based electrodes were studied and compared. Electrochemical impedance analysis reveals the higher electron transport rate in ZnO, but the improved efficiency of TiO2 based DSSC is due to the higher dye loading and fast electron injection. The power conversion efficiencies of the DSSC's fabricated using AMT and AET photosensitizers on ZnO and TiO2NR (NR = nanorod) electrodes are 0.02, 0.03, and 0.23, 0.32 %, respectively. The hydrothermally deposited TiO2nanorod arrays exhibited the highest performance over doctor blade method deposited ZnO based DSSC's. The present study will open a new route to fabricate highly efficient DSSC's using morphologically dependent photoelectrode.