We develop the Double Principal Component Analysis (DPCA) based on a dual factor structure for high-frequency intraday returns data contaminated with microstructure noise. The dual factor structure allows a factor structure for the microstructure noise in addition to the factor structure for efficient log-prices. We construct estimators of factors for both efficient log-prices and microstructure noise as well as their common components, and provide uniform consistency of these estimators when the number of assets and the sampling frequency go to infinity.