Phosphorus (P) deficiency is a common challenge in crop production because of its poor mobility through the soil. The root system plays a significant role in P absorption from the soil and is the initial indicator of low P levels. However, the phenotypic dynamics and longevity of cotton roots under P stress remain unknown. In this study, RhizoPot, an improvised in situ root observation device, was used to monitor the dynamics of root phenotypes of cotton seedlings under P-deficient (PD) and P-replete (PR) conditions. Low P stress reduced P absorption and accumulation in the roots, leading to low dry weight accumulation. Cotton seedlings responded to low P stress by increasing the number of lateral roots, specific root length, branch density, root length density, and length of root hairs. Additionally, the life span of root hairs was prolonged. Low P stress also reduced the average diameter of roots, promoted root extension, expanded the root coverage area, and increased the range of P acquisition. Principal component analysis revealed that the net root growth rate, root length density, root dry weight, P absorption efficiency, average root hair length, and taproot daily growth significantly influenced the cotton root architecture. Collectively, these results show that low P stress reduces the net growth rate of cotton seedling roots and restricts plant growth. Plants respond to P deficiency by extending the life span of root hairs and increasing specific root length and lateral root branch density. This change in root system architecture improves the adaptability of plants to low P conditions. The findings of this study may guide the selection of cotton varieties with efficient P utilization.