The current LiDAR SLAM (Simultaneous Localization and Mapping) system suffers greatly from low accuracy and limited robustness when faced with complicated circumstances. From our experiments, we find that current LiDAR SLAM systems have limited performance when the noise level in the obtained point clouds is large. Therefore, in this work, we propose a general framework to tackle the problem of denoising and loop closure for LiDAR SLAM in complex environments with many noises and outliers caused by reflective materials. Current approaches for point clouds denoising are mainly designed for small-scale point clouds and can not be extended to large-scale point clouds scenes. In this work, we firstly proposed a lightweight network for large-scale point clouds denoising. Subsequently, we have also designed an efficient loop closure network for place recognition in global optimization to improve the localization accuracy of the whole system. Finally, we have demonstrated by extensive experiments and benchmark studies that our method can have a significant boost on the localization accuracy of the LiDAR SLAM system when faced with noisy point clouds, with a marginal increase in computational cost.