The trajectory and dynamics of gut resistome development in the early life of the endangered birds, as well as how they are acquired, remain largely unclear. Here, we present a longitudinal study of the fecal microbiome and resistome of crested ibis (Nipponia nippon) chicks in the first three months of life. In addition, the microbiome and resistome in their parental and living environmental samples were also determined for further exploring the possible factors that could affect their gut resistome. The gut microbiome of ibis chicks contained diverse antibiotic resistance genes (ARGs), dominated by β-lactam, tetracycline, aminoglycoside and macrolide. Novel to this study were the significant, the ARG abundances of ibis chicks were significantly higher than their parents, which would decrease with age. In addition, significant negative correlation between the ARG abundance and microbiome diversity, speculating that the ARG abundances were possibly associated with the gut microbial maturity. Finally, the sourcetracker analysis showed that the microbiota of the ibis parent gut and food were the main sources of ibis chicks microbiota. Collectively, our study showed a trajectory of the resistome and microbiome and the possible influencing factors in the early stage of life in ibises, which would advance our understanding of ARG dynamics in young crested ibis and provide valuable insights into the direction of conservation efforts.