To simulate the sound field based on the real environment, it is essential to know the geometry of room and its acoustic impedances. Recently, the geometry of room can be measured easily using measurements such as Mixed Reality (MR) technology and a laser range finder. However, it is not easy to obtain the acoustic impedances on the surface of rooms by in-situ measurements. On the other hand, with the development of numerical simulation technology, the previous studies have proposed a method for estimating acoustic impedances using the recorded signals from the microphones and sound field simulation. However, for practical use, acoustic impedance estimation that is robust to the errors in the measurement positions is required. In our previous works, we also proposed the measurement system of sound intensities using MR technology. The system can quickly measure the multiple sound intensities and visualizes the measurement results as 3DCG in real time at the measurement position. In this study, we propose the estimation method of acoustic impedances of walls using the measurement of sound intensities at multiple points and FDTD simulation. From the simulations experiments with the positional errors in measurement points, the proposed method improved estimation accuracies by about 30 dB compared to the conventional method with time-signals. In addition, the accuracy was improved by about 8 dB by increasing the number of measurement points.