Background and Aims <p>Intercropping implemented with no-tillage has been recommended as an agricultural strategy to improve crop productivity and soil health. However, limited research has explored the changes in the diversity and abundance of genes related to soil carbon, nitrogen, and phosphorus cycling in a no-till maize/pea intercropping system.</p> Methods <p>An 8-year field experiment was conducted to investigate microbial functional profiles in 0–30 cm soils of maize and pea strips in mono-/intercropping systems under the no-tillage (NT) and conventional tillage (CT) conditions in an arid and semiarid area of China.</p> Results <p>The tillage practices and cropping patterns significantly affected the diversity and abundance of functional genes directly driven by soil properties. Intercropped maize exhibited a significant increase in the abundance of genes (<i>tktA/tktB</i> and <i>rbcL</i>) associated with carbon fixation compared to monocropped maize under the CT or NT condition. Intercropped maize under no-tillage practice significantly reduced the abundance of the CH₄ oxidation gene <i>porB</i> and nitrate reduction gene <i>norB</i>, which restricts greenhouse gas production. Intercropping strips with higher soil nutrient contents than monocropping strips resulted in a reduction in the abundance of genes (<i>gcd</i><i>, </i><i>phoR</i><i>, </i><i>phnJ</i>), which contributed to decreases in inorganic phosphorus solubilization and organic phosphorus mineralization. Consequently, this led to increased phosphorus storage, particularly under the NT condition.</p> Conclusions <p>This research highlights that maize/pea intercropping combined with no-tillage practice is a particularly effective strategy for enhancing nutrient sequestration and reducing emissions in environmentally sustainable agriculture.</p>