Covalent organic frameworks (COFs) exhibit great potential in the application of functional electronic devices. However, there has been no report of the precise fabrication of 3D all-in-one hollow micro/nanostructures based on COFs. Here, for the first time, all-in-one hollow dioxin-based COF-316 microflowers are synthesized measuring 5-7 µm and with interconnected hollow petals through a self-template strategy. The growth mechanism involves the collaborative process of self-assembly of nanoparticles, inside-out Ostwald ripening, and epitaxial growth. Due to the intrinsic porosity and interconnected hollow structure, COF-316 can uniformly composite with polypyrrole (PPy) through the "interior" and "exterior" functionalization, in which the hydrogen bond interaction enhances the charge transfer efficiency and structural stability in the charge/discharge process. The COF-316@PPy flexible transparent supercapacitors exhibit an areal specific capacitance (C A ) of 783.6 µF cm -2 at 3 µA cm -2 and longterm cycling stability. This work will boost research on the valuable design concepts of 3D hollow COF materials for energy storage devices.