How can diffusion models process 3D geometries in a coarse-to-fine manner, akin to our multiscale view of the world?In this paper, we address the question by focusing on a fundamental biochemical problem of generating 3D molecular conformers conditioned on molecular graphs in a multiscale manner. Our approach consists of two hierarchical stages: i) generation of coarse-grained fragment-level 3D structure from the molecular graph, and ii) generation of fine atomic details from the coarse-grained approximated structure while allowing the latter to be adjusted simultaneously.For the challenging second stage, which demands preserving coarse-grained information while ensuring SE(3) equivariance, we introduce a novel generative model termed Equivariant Blurring Diffusion (EBD), which defines a forward process that moves towards the fragment-level coarse-grained structure by blurring the fine atomic details of conformers, and a reverse process that performs the opposite operation using equivariant networks.We demonstrate the effectiveness of EBD by geometric and chemical comparison to state-of-the-art denoising diffusion models on a benchmark of drug-like molecules.Ablation studies draw insights on the design of EBD by thoroughly analyzing its architecture, which includes the design of the loss function and the data corruption process.