Oilseed flax production in northwest China's drylands is constrained by simplistic planting systems and low water productivity. We conducted a three-year field experiment on the semi-arid Loess Plateau to evaluate intercropping as a sustainable intensification strategy. The objective was to assess the effects of different strip configurations in maize/oilseed flax intercropping on system productivity, soil water use, and crop physiological adaptation. A two-factorial randomized block design was used. The treatments comprised three cropping systems (maize monoculture, oilseed flax monoculture, and maize/oilseed flax intercropping) and three strip configurations with specific row ratios: I42 (2 rows of maize: 4 rows of oilseed flax), I63 (3:6), and I84 (4:8). Intercropping significantly increased biomass and grain yield relative to monoculture, with the I84 configuration achieving the highest land equivalent ratio (LER). Soil water storage (0 -80 cm) increased by 8.6% and 6.3% relative to maize and oilseed flax monocultures, respectively. I84 further improved storage by 6.5%-18.9% over narrower configurations. The I84 system alleviated shading stress, leading to significant increases in key photosynthetic parameters of 14.6%-45.2% (P < 0.05) and leaf water use efficiency of 0.8%-44.0% (P < 0.05). These physiological improvements coincided with a rebalancing of endogenous hormones (ABA, CTK, JA, SA). Optimized strip intercropping enhances system productivity by synchronously improving soil water retention and inducing coordinated aboveground-belowground physiological adaptations. This study demonstrates that optimized strip configuration (I84) enhances intercropping productivity by integrating photosynthetic performance, soil water utilization, and hormonal responses in a maize/oilseed flax system.