Today, developing photocatalysts with high sterilization efficiency is still an urgent challenge. Currently photothermal therapy (PTT) and photodynamic therapy (PDT) are known as a promising candidate for eradicating bacteria because of strong reactivity, non-specific attack characteristics and minimal invasiveness. Therefore, the synergic effect of PTT and PDT can shorten the antibacterial time, increase the antibacterial rate, and reduce antibacterial agent dosage. Herein, SnSe samples with sphere, rod, plate, and surface wrinkled morphology were synthesized by a simple solvothermal method. The samples were denoted as SnSe-1, SnSe-2, SnSe-3, and SnSe-4, respectively. The morphology and size of the prepared samples greatly relied on the selection of surfactant and the reaction time. In addition, the size and morphological changes affected the photothermal properties and photodynamic properties of the prepared samples. Among the prepared samples, SnSe-1 showed the best photothermal effect (41.4%) and reactive oxygen species generating ability during the 808 nm laser irradiation. Consequently, SnSe-1 exhibited sterilization rates of 99.99% against Gram-negative Escherichia coli (E. coli) and Gram-positive Bacillus subtilis (B. subtilis) during NIR irradiation (1.5 W/cm2, 10 min) at a relatively low concentration (25 mu g/mL). The result suggests that SnSe-1 nanoparticle with a spherical shape could be used as an effective antibacterial agent for the treatment of bacterial contamination, including rapid bacterial sterilization in water.