Nitrous oxide (N2O) is a potent greenhouse gas; thus, understanding its emission mechanisms from agricultural soils is a critical research priority. Previous studies have largely focused on macro-scale drivers like climate and management, leaving a gap in the systematic understanding of how micro-scale soil pore heterogeneity regulates N2O dynamics. This review addresses this gap by synthesizing current knowledge. It first examines how dynamic changes in soil pore characteristics (e.g., porosity, pore-size distribution, connectivity) govern the transport of water, gases (O2, N2O), and solutes, thereby creating distinct microenvironments for N2O production and diffusion. A key focus is the scenario of straw incorporation. The analysis details how straw management, encompassing application methods, duration, and straw type—interacts with soil physical structure and moisture regimes (particularly wetting-drying cycles) to reshape pore network heterogeneity. Building on this physical foundation, the review then analyzes the consequential biogeochemical effects. It highlights how pore-scale heterogeneity in the distribution and accessibility of carbon/nitrogen substrates and oxygen critically regulates microbial nitrogen transformation processes (e.g., nitrification and denitrification), ultimately controlling N2O production pathways and the emergence of emission “hotspots.” Furthermore, this synthesis consolidates potential micro-scale mitigation strategies that leverage pore structure manipulation. These include optimizing straw treatment (e.g., biochar production, particle size reduction) and targeting microbial communities to design microenvironments that suppress N2O formation or enhance its reduction to N2. In summary, by developing an integrated framework that links pore structure dynamics with microbial biogeochemistry, this review advances the mechanistic understanding of N2O emissions under straw incorporation. It provides a novel, pore-centric perspective and a theoretical basis for designing innovative farmland management practices aimed at reducing greenhouse gas emissions while supporting sustainable agriculture.