InGaN quantum dots (QDs) deposited on Si Nx nanomasks have been investigated by atomic force microscopy, photoluminescence (PL), and photoluminescence excitation (PLE) measurements. It was found that the size of QDs can be well controlled by Si Nx nanomasks, enabling the manipulation of quantum confinement effect. The PL spectra of InGaN QDs contain several fine structures, and the main peaks can be attributed to families of QDs with different sizes. The emission arising from InGaN QDs and GaN buffer layer can be clearly distinguished based on PLE measurement, which can be used to improve the interpretation in the previous reports. Our study indicates that the quantum confined Stark effect due to piezoelectric field plays a very important role in the optical properties of InGaN QDs, which is very useful for the application of optoelectronic devices.