Jet pump cavitation reactors (JPCRs) have significant potential to be used in water treatment applications. During their operation, the hydroxyl radicals generated by cavitation collapse produce a strong oxidation capacity, which is one of the key mechanisms in disrupting algal cells. In this paper, we investigate the hydroxyl radicals produced by single cavitation bubble in a JPCR. The numerical method includes a bubble dynamic model, molecular diffusion model, energy balance equation, and chemical reaction model for predicting the hydroxyl radical production. Additionally, the pressure distribution within a JPCR is tested and used to analyze the single-bubble performance. The effects of the JPCR operating conditions and structure parameters on hydroxyl radical production are further discussed. Our results indicate that, when the flow rate ratio is positive, the number of hydroxyl radicals is closely related to the development and collapse of the cavitation bubble and reaches a peak value under the critical condition. When the flow rate ratio is negative, the maximum production of hydroxyl radicals appears under backflow stagnation condition. In general, increasing the throat length–diameter ratio and diffuser angle encourages the production of hydroxyl radicals, whereas increasing the area ratio inhibits their generation.