Separation and recovery of metal ions from wastewater is greatly significant because of the non‐negligible harm of heavy metal ions in water to human health and environment. A water‐stable aluminum‐based metal–organic framework material (MOF‐303) with native N adsorption sites is proposed for the selective adsorption and separation of the mixture with heavy metal ions (Fe3+ and Cr3+). This type of material comprises the native N adsorption sites, evenly distributing on the organic linking group. It means that the adsorbent has a smoother transport channel for metal ion, resulting in high adsorption capacity and selectivity. The single‐component adsorption results show that MOF‐303 has excellent adsorption capacity for Fe3+, up to a maximum adsorption capacity of 104 mg·g−1, which is about 5 times more than the counterpart capacity of Cr3+. Comprehensive separation studies show that the separation of the mixture with these ions can be achieved in the pH range of 1–3, and the selective adsorption is the most efficient. During 30 min of adsorption process, the removal rate of Fe3+ can be attained by 90%. And the adsorption property of this material can be recovered effectively through pickling process. In addition, the adsorption mechanism of MOF‐303 is characterized by zeta potential analysis, X‐ray photoelectron spectroscopy (XPS), and Fourier transform infrared (FT‐IR). Our work shows that MOF‐303 is not only a promising material for effective separation of Fe3+ from industrial wastewater but also providing a new perspective the specific adsorption capacity of MOF materials.