This study introduces a novel Swiss-roll micro-combustor design that employs a non-premixed counterflow flame for efficient and stable micro-combustion. This design addresses practical system challenges by (1) stabilizing the flame, (2) enhancing heat recovery and gas preheating, (3) aligning gas momentum with the exhaust, and (4) minimizing disruptive fluid motion within the channels. This research investigates the dynamic behavior and combustion characteristics of a methane-oxygen flame within the combustor across a range of equivalence ratios (1.50–3.38). A synergistic approach combining flame dynamics analysis, spectroscopy, and RGB image processing explores the interplay between flame temperature, strain rate, and equivalence ratio. The results demonstrate the effectiveness of the RGB method as a cost-efficient tool for predicting variations in C2∗ and CH∗ radicals and light-intensity radiations. While flame thickness and length exhibit complex dependencies on the fuel-to-oxygen ratio and wall temperature, specific radical emissions vary dynamically with the equivalence ratio. Notably, equivalence ratios of 1.94 and 2.26 exhibit minimal temporal variations in flame properties, suggesting optimal stability and predictability for practical applications. The investigated flame is classified as a “cool flame,” and efficiency declines with richer mixtures due to increased exhaust heat loss and incomplete combustion. This work paves the way for further micro-combustor design optimization and unlocks the potential of non-premixed counterflow flames in diverse micro-scale applications.