Covalent organic frameworks (COFs) have been used for electrocatalytic oxygen reduction reaction (ORR) due to their structural tunability, well-defined electroactive sites, and easy introduction of heteroatoms. Researchers have incorporated heteroatoms into COF architectures to enhance their performance by tuning the electronic environment of oxygen intermediates. However, only a few heteroatoms (O, S, N, P) have been introduced into the backbone of COFs, and the effects of different types of heteroatoms on the electronic structure of COFs have not been specifically investigated. Furthermore, the development of COF electrocatalysts with highly active ORR is still at an early stage. Herein, we report a series of metal-free benzotrithiophene-based COFs containing various heteroatoms (Se, S or O), BTT-COFs (named JUC-616, JUC-617, and JUC-618, respectively), and explore their ORR catalytic activity. Remarkably, JUC-616 involving precise Se atoms exhibits a half-wave potential of 0.78 V and a high turnover frequency (TOF) of 0.0062 s−1 at 0.75 V vs. the reversible hydrogen electrode (RHE), which is the best among the metal- and pyrolysis-free COF-based electrocatalysts reported so far. Thus, this work shows the promising potential of functionalized COFs with precise heteroatoms for electrocatalysis.