Single crystalline nanoclusters and nanorods like structure of barium borate (β- BaB2O4) were synthesized by organic free hydrothermal method at various reaction times of 8, 24 and 48 h. XRD shows the formation of pure and single phase of β- BaB2O4 with improved crystallinity at elevated reaction time. β- BaB2O4 crystallizes in hexagonal system with lattice parameter a=b=12.53 Å and c=12.72 Å. The surface morphology picturizes the formation of nanoclusters and rod structures with several micrometer length and nanometer diameter. By increasing the reaction time and due to prolonged pressure, aggregation followed by elongation resulted in the transformation of nanoclusters into rod like structure. The nanostructured barium borates possess strong UV absorbance and wide optical window. The nonlinear optical studies by Z– scan technique shows the material to possess saturable absorption and self-defocusing nature. A strong variation in third order nonlinear optical parameters with change in the morphology of β- BaB2O4 was observed. Also β- BaB2O4 rod like structure is identified to be more efficient optical limiters in the green regime of continuous wave lasers. © 2016 Elsevier Ltd