The surface reconstructions of decapped InAs(001) and In₀.₅₃Ga₀.₄₇As(001) have been studied using scanning tunneling microscopy (STM). Quantitative comparison of the In₀.₅₃Ga₀.₄₇As(001)-(4x2) and InAs(001)-(4x2) show the reconstructions are almost identical, but In₀.₅₃Ga₀.₄₇As(001)-(4x2) has at least a 4x higher surface defect density even on the best samples. For both In₀.₅₃Ga₀.₄₇As(001)-(4x2) and InAs(001)-(4x2), density functional theory (DFT) simulations at elevated temperature are consistent with the experimentally observed 300 K structure being a thermal superposition of three structures. The passivation of InAs(001) and InGaAs(001) surface using three different oxides (SiO, Ga₂O and In₂O) was studied using STM, STS, and DFT modeling of bonding and electronic structures. SiO molecules have higher self-binding energy so that they bond themselves and form nanoclusters on InAs(001)-(4x2) surface. Conversely, both Ga₂O and In₂O molecules bond to the As atoms at the edge of the rows. However, Ga2O molecules also bond to preexisting Ga₂O oxide on the surface. At full coverage with post-deposition annealing, SiO oxide remains as nanoclusters, Ga₂O oxide forms disordered structures with the large flat terraces on the surface, while In₂O oxide bonds with the trough In atoms to form new O-In bonding sites and forms ordered structures running in the [110] direction on In₀.₅₃Ga₀.₄₇As(001)-(4x2). STS results show that Ga₂O oxide does not passivate the interface nor unpin the In₀.₅₃Ga₀.₄₇As(001)-(4x2) surface consistent with its inability to form monolayer ordered islands on the surface; conversely, In₀.₅₃Ga₀.₄₇As(001)-(4x2) has an ordered monolayer coverage and is unpinned