Indoxyl sulfate is a protein-bound uremic toxin synthesized from indole that cannot be efficiently removed by the hemodialysis method and thus becomes a key risk factor for the progression of chronic kidney disease. Here, we develop a non-dialysis treatment strategy to fabricate an ultramicroporous olefin-linked covalent organic framework with high crystallinity in a green and scalable fashion for selectively removing the indoxyl sulfate precursor (i.e., indole) from the intestine. Various analyses show that the resulting material exhibits excellent gastrointestinal fluid stability, high adsorption efficiency, and good biocompatibility. Notably, it realizes the efficient and selective removal of indole from the intestine and significantly attenuates serum indoxyl sulfate level in vivo. More importantly, the selective removal efficacy of indole is substantially higher than that of the commercial adsorbent AST-120 used in the clinic. The present study opens up a new avenue to eliminate indoxyl sulfate by a non-dialysis strategy and further expands the in vivo applications of covalent organic frameworks.