Recently, InGaN/GaN quantum wells with different nanostructures such as nanoholes and nanorods have been proposed to enhance the light emitting efficiency. This paper calculates the influence of nanostructures to the strain and band profile of the quantum well. The effects of strain relaxation and surface states are analyzed, which could possibly influence the diode emission properties. Our calculation results show that the strain relaxation and the surface state pinning play important roles in enhancing the light emission, reducing the quantum confined Stark effect, and causing the blue shift of the spectrum. Our calculation results provide useful information in analyzing emission properties of nanohole arrays and similar structures.