In addition to microstructure noise, the presence of multiple transactions at each recording time is another common feature for high-frequency data.In this paper, we consider the estimation of integrated covariance (ICV) matrix for multiple high-frequency data in a high-dimensional situation where the number of stocks and the "effective" sample size go to infinity proportionally.First, we study the limiting spectral behavior of a pre-averaged version of averaged time-variation adjusted realized covariance (PA-ATVA) matrix based on multiple noisy observations. We show that the PA-ATVA matrix has several desirable properties: it eliminates the effects of microstructure noise and multiple transactions; it allows for rather general dependence structure in the noise process, both cross-sectional and temporal; its LSD depends solely on that of ICV matrix through the Marčenko-Pastur equation. Furthermore, we show that all the aforementioned properties still hold in the presence of asynchronicity. Second, we further propose a nonlinear shrinkage estimator of the ICV matrix based on the PA-ATVA matrix. We show that the proposed estimator is not only asymptotically positive-definite, but also enjoys a desirable estimation efficiency.