This study aimed to achieve effective in vivo detoxification of deoxynivalenol (DON) contained in piglet feedstuff by developing sodium metabisulfite (SMBS)-containing Eudragit L100-55 (ES) microparticles as a novel feed additive. DON detoxification was assessed in vitro (IPEC-J2 cell) and in vivo (piglet). Within 2 h of exposure to simulated gastric fluid (SGF), 14.31% of encapsulated SMBS was released from ES microparticles, while 82.93% was released in another 80 min in simulated intestinal fluid (SIF). In IPEC-J2 cells, 0.1% ES microparticles remediated the toxicity of DON after 2 h incubation in SGF and 40 min in SIF. Forty weaned piglets with similar body weights (10 pigs/treatment) were fed for 28 days. Four diets were used: negative control (NC, 0.00 ppm DON), positive control (PC, 3.33 ppm DON), pure SMBS (PST, 3.33 ppm DON and 0.2% SMBS), and ES microparticles (EST, 3.33 ppm DON and 0.40% ES microparticles). The PC diet reduced ADG by 21.4% and ADFI by 20.1% compared to the NC diet (P < 0.05). The EST diet increased ADG and ADFI by 21.7% and 17.7% compared to the PC diet (P < 0.05), with no significant difference from the NC diet (P > 0.05). Compared to the PC and PST diets, the EST diet increased villus height, villus height/crypt depth ratio, mRNA levels of claudin 3 and peptide transporter 1, and decreased mRNA level of toll-like receptor 4 (P < 0.05). ES microparticles could protect SMBS, and the released SMBS could mitigate the toxic effects of DON in piglets.