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Thermochromic behaviors of VO2(M) are affected significantly by the size purity, and crystallinity of the particles, and it needs a mass of experiments to adjust the factors suitably. Herein, an orthogonal array design (OAD) [L9 (34)] was applied to select the optimum conditions for high-throughput preparation of VO2(M) nanoparticles with controllable morphology and size. The effects of fill ratio, reaction time, annealing time, and annealing temperature on the size of VO2(M) nanoparticles were evaluated by OAD. These results showed that the factors for the size arranged as follows: fill ratio > reaction time > annealing time > annealing temperature. The validation of optimized experimental parameters proved that pure VO2(M) nanoparticles with a diameter of ∼60 nm were prepared in this work. Therefore, the high-throughput preparation of VO2(M) nanoparticles with small size was achieved via an optimized two-step hydrothermal synthesis method, which can support the large-scale applications of VO2(M) nanoparticles in smart windows and optical switches.