Data integrity is important for non-volatile memory (NVM) systems that maintain data even without power. The data integrity in NVM is possibly compromised by integrity attacks, which can be defended against by integrity verification via integrity trees. After NVM system failures and reboots, the integrity tree root is responsible for providing a trusted execution environment. However, the root often becomes a performance bottleneck, since updating the root requires high latency on the write critical path to propagate the modifications from leaf nodes to the root. The root and leaf nodes have to ensure the crash consistency between each other to avoid any update failures that potentially result in misreporting the attacks after system reboots. In this paper, we propose an efficient and low-latency scheme, called SCUE, to directly update the root on the SGX integrity tree (SIT) by overlooking the updates upon the intermediate tree nodes. The idea behind SCUE explores and exploits the observation that only the persistent leaf nodes and root are useful to ensure the integrity after system failures and reboots, due to the loss of the cached intermediate tree nodes. To achieve the crash consistency between root and leaf nodes, we accurately predict the updates upon the root and pre-update the root before the leaf nodes are modified. Moreover, the SIT root is difficult to be reconstructed from the leaf nodes since updating one tree node needs its parent node as input. We use a counter-summing approach to reconstructing the SIT from leaf nodes. Our evaluation results show that compared with the state-of-the-art integrity tree update schemes, our SCUE scheme delivers high performance while ensuring the system integrity.