Water-fertilizer strategies (WFS) are considered an important means of regulating greenhouse gas (GHG) emissions from croplands. However, existing evidence has mostly focused on surface fluxes, and the regulatory mechanisms by which dissolved organic matter (DOM) and microorganisms jointly affect GHG production and emission remain poorly understood. Based on this, we conducted an indoor soil-column experiment with high water and no fertilization as the control (CK), and established five WFS treatments by crossing two irrigation levels (high water, I_H; low water, I_L) with two fertilization levels (high fertilizer, F_H; low fertilizer, F_L). We quantified the temporal dynamics of surface fluxes and the diffusion fluxes of CO₂, CH₄, and N₂O in topsoil (0–10 cm) and subsoil (10–20 cm), and identified potential process-level pathways associated with gas production, transport, and emission under controlled soil-column conditions. WFS induced both temporal fluctuations and pronounced vertical differentiation of GHGs, with the subsoil exhibiting the lowest diffusion fluxes and cumulative diffusion. Among the three gases, N₂O was the most sensitive to WFS; fertilization increased peak N₂O fluxes at the surface and in topsoil to 2.02–2.47 and 4.50–13.46 times those under CK, respectively. The maximum cumulative CO₂ emission/diffusion occurred under I_H at the surface, under I_L in topsoil, and under I_H in subsoil. Furthermore, DOM quality and archaeal responses were identified as important process-related indicators linking WFS-driven changes in soil physical status with substrate redistribution, thereby potentially influencing GHG emission pathways along the profile. Notably, surface CO₂ and N₂O emissions were significantly associated with diffusion processes in subsoil and topsoil, respectively. These findings highlight that mitigation-oriented irrigation and fertigation assessment should incorporate profile gas diffusion constraints, DOM indicators, and archaeal responses to better diagnose GHG risks under WFS.