Methanotroph-based CH4 conversion technology is a promising alternative to conventional CH4 utilization methods that rely on energy-intensive CO2 capture processes. In this study, we introduce a novel CH4 capture, utilization, and sequestration (MCUS) technology as a proof-of-concept for eco-friendly CH4 conversion that is applicable to various methanotroph strains. We validated this hypothesis by evaluating ectoine production in Methylotuvimicrobium alcaliphilum 20Z. Cultivation experiments were conducted using pure O2 pulse injection to facilitate the separation of the CO2 generated during CH4 oxidation by concentrating it. To verify the MCUS concept systematically, we performed a model-based process analysis. The operational strategies for the reactors were developed using experiment-based kinetics and reactor models, followed by the design of a rigorous process flow diagram. Economic and environmental impact analyses were conducted to compare MCUS with air-based cultures and existing oxidative CH4 conversion technologies. The key advantage of MCUS is its significantly lower CO2 emissions (0.71 kg-CO2 eq/kg-CH4) than oxidative CH4 utilization (>2.75 kg-CO2 eq/kg-CH4). Moreover, the net present value per CH4 molecule was estimated at 0.7 $/kg-CH4, substantially higher than existing oxidative conversion methods (0.03 $/kg-CH4). Additionally, compared with air-based cultivation, the MCUS process exhibits superior economic and environmental performances. We used methanotrophs for CH4 “capture” and “utilization,” effectively leveraging “sequestration” to convert emissions into pure CO2. The proposed MCUS technology holds promise for practical applications of methanotrophs in producing various high-value-added products, emphasizing eco-friendly approaches.