Obtaining cost-effective iron (oxyhydr)oxide nanocrystallines is the essential prerequisite for their future extensive applications in environmental remediation, such as the removal of heavy metals from contaminated waters. Here, various phases of iron (oxyhydr)oxide nanocrystallines were simply synthesized from the phase-controlled transformation of amorphous hydrous ferric- or ferrous-oxide in thermal solution with a certain ethanol/water ratio and with the presence of oleic acid. According to this method, goethite nanorods in diameter of 3–4 nm, hematite nanocubes sized 20–30 nm, and magnetite nanoparticles in diameter of 6–7 nm were successfully obtained. The final products of this transformation can be conveniently controlled by adjusting the reaction parameters, such as pH, temperature, and ethanol/water ratio. Due to the enhanced specific surface area and probably the modifications of the surface structure of nanocrystallines, the as-synthesized goethite nanorods and magnetite nanoparticles demonstrated extremely strong As(III) affinity, with 5.8 and 54 times of As(III) adsorption, respectively, higher than the micron-sized relatives. The cost-effective feature of as-synthesized nanocrystallines and their remarkably enhanced affinity toward arsenic made them potentially applicable for the removal of arsenic and such like heavy metals from the contaminated environment.