In0.53Ga0.47As is an important material for the shortwave near-infrared negative electron affinity photocathodes. Zn atoms were doped in the intrinsic InGaAs to form p-type In0.53Ga0.44 Zn0.03As emission layer. Models of Zn-doped In0.53Ga0.44 Zn0.03As bulk with In, Ga or As vacancy defect were built in the article. Emphasis was put on how the defects influence the microstructure and the optical properties of the Zn-doped InGaAs emission layer. Combined effect of both vacancy defects and doped Zn atoms for the photoelectron emission performance was further studied. It is indicated that the In or Ga vacancy defect is easier to be generated than the As from the analysis of formation energy. However, As vacancy defect is more benefit for photoelectrons emission considering the material polarity because As vacancy defect interacting with doped Zn atoms is a positive center and generates acceptor level to narrow the energy gap. At the same time Zn ion will be easier to accept electrons when the As vacancy defect appears. The absorption coefficient of the InGaAs emission layer with As vacancy defect is also bigger than that with In or Ga defect. In conclusion, As vacancy defect is benefit and will promote the photoemission of InGaAs photocathode while the In or Ga vacancy defect should be avoided when the emission layer is grown.