Ribosome biogenesis, taking place mainly in the nucleolus, involves coordinated expression of pre-ribosomal RNAs (pre-rRNAs) and ribosomal proteins, pre-rRNA processing, and subunit assembly with the aid of numerous assembly factors. Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing; however, the molecular mechanism remains unknown. Here we report that AtPRMT3 interacts with Ribosomal Protein S2 (RPS2) facilitating the 90S/Small Subunit (SSU) processome processing and repressing nucleolar stress. We isolated an intragenic suppressor of atprmt3-2 bearing the entire N-terminus but lacking an intact enzymatic activity domain of AtPRMT3, which rescued the developmental defects of atprmt3-2. RPS2 was further identified as an interacting partner of AtPRMT3, and loss-of-function rps2a2b mutants were reminiscent of atprmt3 phenotypically, including pleiotropic developmental defects and aberrant pre-rRNA processing. RPS2B bound directly to pre-rRNAs in the nucleus, and such binding was enhanced in atprmt3-2. Consistently, multiple components of 90S/SSU processome were more enriched by RPS2B in atprmt3-2, which causes early pre-rRNA processing defects and nucleolar stress. Our study uncovered a novel mechanism by which AtPRMT3 cooperates with RPS2B to facilitate the dynamic assembly/disassembly of the 90S/SSU processome during ribosome biogenesis and repress nucleolar stress.