This article studies a high-dimensional factor model with sparse idiosyncratic covariance matrix in continuous time, using asynchronous high-frequency financial data contaminated by microstructure noise. We focus on consistent estimations of the number of common factors, the integrated covariance matrix and its inverse, based on the flat-top realized kernels introduced by Varneskov. Simulation results illustrate the satisfactory performance of our estimators in finite samples. We apply our methodology to the high-frequency price data on a large number of stocks traded in Shanghai and Shenzhen stock exchanges, and demonstrate its value for capturing time-varying covariations and portfolio allocation.