Myosin Ⅱ plays multiple roles in physiological and pathological functions through its ATPase activity. The present study was designed to optimize a micro-assay of myosin Ⅱ ATPase activity based on molybdenum blue method, using a known myosin Ⅱ ATPase inhibitor, blebbistatin. Several parameters were observed in the enzymatic reaction procedure, including the concentrations of the substrate(ATP) and calcium chloride, p H, and the reaction and incubation times. The proportion of coloration agent was also investigated. The sensitivity of this assay was compared with the malachite green method and bioluminescence method. Additionally, 20 natural compounds were studied for myosin Ⅱ ATPase inhibitory activity using the optimized method. Our results showed that ATP at the concentration of 5 mmol·L~(-1) and ammonium molybdate : stannous chloride at the ratio of 15 : 1 could greatly improve the sensitivity of this method. The IC50 of blebbistatin obtained by this method was consistent with literature. Compound 8 was screened with inhibitory activity on myosin Ⅱ ATPase. The optimized method showed similar accuracy, lower detecting limit, and wider linear range, which could be a promising approach to screening myosin Ⅱ ATPase inhibitors in vitro. Myosin Ⅱ plays multiple roles in physiological and pathological functions through its ATPase activity. The present study was designed to optimize a micro-assay of myosin Ⅱ ATPase activity based on molybdenum blue method, using a known myosin Ⅱ ATPase inhibitor, blebbistatin. Several parameters were observed in the enzymatic reaction procedure, including the concentrations of the substrate (ATP) and calcium chloride, p H, and the reaction and incubation times. The proportion of coloration agent was also investigated. The sensitivity of this assay was compared with the malachite green method and bioluminescence method. Additionally, 20 natural compounds were studied for myosin Ⅱ ATPase inhibitory activity using the optimized method. Our results showed that ATP at the concentration of 5 mmol·L -1 and ammonium molybdate: stannous chloride at the ratio of 15: 1 could substantially improve the sensitivity of this method. The IC50 of blebbistatin was by this method was consistent w ith literature. Compound 8 was screened with inhibitory activity on myosin II ATPase. The optimized method showed similar accuracy, lower detecting limit, and wider linear range, which could be a promising approach to screening myosin II ATPase inhibitors in vitro.