Phosphorus pollution caused by animal husbandry is becoming increasingly problematic, especially where decreasing and non-renewable phosphorus resources are concerned. We investigated the growth performance, bone development, phosphorus metabolism and gut microbiota changes elicited by different phosphorus levels with/without phytase in chicks during the brooding period (1–42 d). Five-hundred-and-forty (540) egg-laying chickens were assigned to six groups (0.13% NPP, 0.29% NPP, 0.45% NPP, 0.13% NPP + P, 0.29% NPP + P and 0.45% NPP + P) according to a factorial design with three non-phytate phosphorus (NPP) levels (0.13, 0.29 and 0.45%) and two phytase (P) dosages (0 and 200 FTU/kg). Chicks fed with the diet with 0.13% NPP had the lowest body weight, average daily gain, shank length, average daily feed intake and highest ratio of feed to gain, while phytase supplementation was able to mitigate the adverse effects of low-phosphorus diets on growth performance. Moreover, phosphorus metabolism was affected by different dietary NPP and phytase levels. Thus, 0.13% NPP significantly reduced serum phosphorus, while phytase supplementation significantly increased serum phosphorus. Notably, phosphorus utilization in the 0.13% NPP group was significantly decreased and the phosphorus excretion ratio was increased. Phytase supplementation significantly improved phosphorus utilization by 43.79% and decreased phosphorus emission in the 0.13% NPP group but not in the 0.29% NPP or the 0.45% NPP group. Remarkably, the alpha diversity of gut microbiota was significantly decreased in the low-phosphorus group, while phytase supplementation increased alpha diversity and improved gut microbial community and function. The LEfSe analysis revealed that several differential genera (e.g., Bacteroides, norank_f__Clostridiales_vadinBB60_group and Eggerthella) were enriched in the different dietary NPP and phytase levels. Furthermore, correlations between differential genera and several crucial phenotypes suggested that the enrichment of beneficial bacteria with different levels of phosphorus and phytase promoted phosphorus utilization in the foregut and hindgut. In summary, low-phosphorus diets inhibited growth performance and bone development, decreased utilization of phosphorus and altered gut microbial structure and function in the brooding stage of chicks. Finally, phytase supplementation improves growth performance and bone development and decreases phosphorus emission, and the potential mechanisms may be associated with the reprogramming of gut microbiota.