Microchannel heat exchangers are widely employed in high heat flux scenarios due to their high compactness and heat transfer efficiency. However, the laminar flow dominance within them leads to the thickening of the thermal boundary layer, which limits further enhancement of thermal performance. This paper aims to systematically investigate, via numerical simulation, the impact of key geometric parameters (shape, size, and spacing) of baffle structures on the flow and heat transfer characteristics within microchannels, to identify the design that optimizes the overall performance evaluation criterion (PEC). A three-dimensional conjugate heat transfer model was developed. Numerical simulations were conducted over a Reynolds number (Re) range of 477 to 1454. The results indicate that among the three shapes of protrusions and cavities studied-rectangular, triangular, and semi-circular-the semi-circular protrusion baffle achieves the highest PEC of up to 1.098. Its streamlined profile effectively disrupts the thermal boundary layer and induces vortices while maintaining a favorable pressure drop. Regarding size, the highest PEC values were generally observed when the ratio of the total baffle height to the channel width was 0.5. For the arrangement, a spacing of three times the baffle height yielded the optimal performance, with a peak PEC of 1.242, whereas closer spacing resulted in deteriorated overall performance due to a significant pressure drop penalty. Based on the optimal parameter combination, an empirical Nu-Re correlation was established for performance prediction. This study provides a theoretical foundation and optimization strategy for the design of high-performance microchannel heat exchangers.