Diminishing soil fertility and crop productivity due to traditional intensive cultivation has prompted the use of straw and manure to improve soil health in Northeast China. However, few comparative studies have explored the influence of varying straw and manure incorporation depths on crop growth. A field experiment in the rainfed black soil regions of Gongzhuling and Keshan assessed the effects of deep (30 cm) and shallow (15 cm) incorporations of straw and manure on soil fertility, maize root growth, and maize productivity. Deep incorporations, via subsoiling tillage (DST) and deep-plow (DDT) tillage, enhanced soil water storage of 30–100 cm soil layer during periods of low rainfall, improved the availability of nutrients (nitrogen, phosphorus, and potassium) and soil organic matter content, especially in deeper soil, compared to shallow incorporation using rotary tillage (SRT). Both DST and DDT induced a larger rooting depth and a higher fine root (diameter class 0–0.5 mm) length density by 31.0% and 28.9%, respectively, accompanied by reduced root turnover. Furthermore, the sub-surface foraging strategies of roots under the DST and DDT treatments boosted the total nitrogen, phosphorus, and potassium uptake (6.5–17.9%) and achieved a higher dry mass accumulation during the later growth period, thus leading to notable improvements in the 100-kernel weight and yield (16.1–19.7%) and enhancing water- and nutrient-use efficiencies by 2.5–20.5%. Overall, compared to shallow incorporation, deep incorporation of straw and manure significantly enhances root growth and spatial distribution of soil water and nutrients, which has great potential for increasing maize yield in rainfed agricultural areas.