Several large volatility matrix estimation procedures have been recently developed for factor-based It processes whose integrated volatility matrix consists of low-rank and sparse matrices. Their performance depends on the accuracy of input volatility matrix estimators. When estimating co-volatilities based on high-frequency data, one of the crucial challenges is non-synchronization for illiquid assets, which makes their co-volatility estimators inaccurate. In this paper, we study how to estimate the large integrated volatility matrix without using co-volatilities of illiquid assets. Specifically, we pretend that the co-volatilities for illiquid assets are missing, and estimate the low-rank matrix using a matrix completion scheme with a structured missing pattern. To further regularize the sparse volatility matrix, we employ the principal orthogonal complement thresholding method (POET). We also investigate the asymptotic