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The evolution of canopy traits related to maize yield increases has been well documented, but the changes in the root system over decades and their relationships with the water use efficiency (WUE) and nitrogen (N) use efficiency (NUE) require further investigation. In this study, we analyzed the morphological and physiological characteristics of the roots, as well as the water-N uptake, WUE, and NUE under low water/N (LW/LN) and high water/N (HW/HN) supply levels in 11 elite inbred maize lines released in China during the 1960s, 1980s, and 2000s. The results showed that yield improvement in the inbred lines from the 1960s to the 1980s (61–109%) was greater than that in those from the 1980s to the 2000s (6–17%), and the resistance to drought and low N also exhibited a significant linear increase over the decades. The utilization of water and N by the inbred lines evolved efficiently and economically, especially in stressful environments. The improved WUE of modern inbred lines was demonstrated by the higher yield and lower evapotranspiration. The NUE defined as the grain yield obtained per unit of N in plants increased in a linear manner over the three decades, and it was accompanied by higher N accumulation in the grains and greater N translocation efficiency in the roots. However, the agronomic N use efficiency improved from the 1960s to the 1980s, but then decreased from the 1980s to the 2000s. The modern inbred lines tended to produce less redundant roots in the top (0–20 cm) soil layer, whereas root development was enhanced in the deeper soil layer. The morphological properties of the roots (dry weight, length, volume, surface area, weight density, and length density) tended to increase from the 1960s to the 1980s but then decreased from the 1980s to the 2000s, and they had significant quadratic relationships with the yield, WUE, and NUE. By contrast, water/N amount absorbed per unit root volume, the physiological properties related to the root absorption area, root activity improved over the decades, where the physiological properties had positive linear relationships with the yield, WUE, and NUE. Thus, we conclude that the maize roots evolved alongside higher yields and greater tolerance to drought and low N environments. The improved WUE and NUE in the modern inbred lines were associated with the greater physiological absorption capacity of the roots rather than larger root size in normal or stressful environments.