Atomic-scale nanofacets were observed in semipolar (202̄1̄) and (202̄1) InGaN quantum wells (QWs)/GaN quantum barriers interfaces. Transmission electron microscopy studies showed that these nanofacets were mainly composed of (101̄1), (101̄1)and (101̄1) planes, which led to significant fluctuations in QW thickness. Atom probe tomography studies were carried out to visualize the nanofacet structure. The In composition in the InxGa1-xN alloys followed a binominal distribution despite the formation of the nanofacet structure. One-dimensional (1D) Schr{"odinger- Poisson drift-diffusion simulation showed that these nanofacets and associated QW thickness fluctuations will lead to a large wavelength shift and a broadened spectral linewidth for semipolar QWs.