Due to the mechanism of recording, the presence of multiple transactions at each recording time becomes a common feature for high-frequency data in financial market. Using random matrix theory, this paper considers the estimation of integrated covariance (ICV) matrices of high-dimensional diffusion processes based on multiple high-frequency observations. We start by studying the estimator, the time-variation adjusted realized covariance (TVA) matrix, proposed in Zheng and Li (2011) without microstructure noise. We show that in the high-dimensional case, for a class C of diffusion processes, the limiting spectral distribution (LSD) of averaged TVA depends not only on that of ICV, but also on the numbers of multiple transactions at each recording time. However, in practice, the observed prices are always contaminated by the market microstructure noise. Thus the limiting behavior of pre-averaging averaged TVA matrices is studied based on the noisy multiple observations. We show that for processes in class C, the pre-averaging averaged TVA has desirable properties that it eliminates the effects of microstructure noise and multiple transactions, and its LSD depends solely on that of the ICV matrix. Further, three types of nonlinear shrinkage estimators of ICV are proposed based on high-frequency noisy multiple observations. Simulation studies support our theoretical results and show the finite sample performance of the proposed estimators. At last, the high-frequency portfolio strategies are evaluated under these estimators in real data analysis.