Current self-supervised learning (SSL) methods (e.g., SimCLR, DINO, VICReg, MOCOv3) target primarily on representations at instance level and do not generalize well to dense prediction tasks, such as object detection and segmentation. Towards aligning SSL with dense predictions, this paper demonstrates for the first time the underlying mean-shift clustering process of Vision Transformers (ViT), which aligns well with natural image semantics (e.g., a world of objects and stuffs). By employing transformer for joint embedding and clustering, we propose a bi-level feature clustering SSL method, coined Feature-Level Self-supervised Learning (FLSL). We present the formal definition of the FLSL problem and construct the objectives from the mean-shift and k-means perspectives. We show that FLSL promotes remarkable semantic cluster representations and learns an embedding scheme amenable to intra-view and inter-view feature clustering. Experiments show that FLSL yields significant improvements in dense prediction tasks, achieving 44.9 (+2.8)% AP and 46.5% AP in object detection, as well as 40.8 (+2.3)% AP and 42.1% AP in instance segmentation on MS-COCO, using Mask R-CNN with ViT-S/16 and ViT-S/8 as backbone, respectively. FLSL consistently outperforms existing SSL methods across additional benchmarks, including UAV object detection on UAVDT, and video instance segmentation on DAVIS 2017. We conclude by presenting visualization and various ablation studies to better understand the success of FLSL. The source code is available at https://github.com/ISL-CV/FLSL.