Homologous recombination plays a central role in guaranteeing chromosome segregation during meiosis. The precise regulation of the resolution of recombination intermediates is critical for the success of meiosis. Many proteins, including the RECQ DNA helicases (Sgs1/BLM) and Topoisomerase 3α (TOP3α), have essential functions in managing recombination intermediates. However, many other factors involved in this process remain to be defined. Here we report the isolation of meiotic chromosome association 1 (MEICA1), a novel protein participating in meiotic recombination in rice (Oryza sativa). Loss of MEICA1 leads to non-homologous chromosome association, the formation of massive chromosome bridges, and fragmentation. MEICA1 interacts with MSH7, suggesting its role in preventing non-allelic recombination. In addition, MEICA1 has an anti-crossover activity revealed by suppressing the defects of crossover formation in msh5 meica1 compared with that in msh5, showing the similar function with its interacted protein TOP3α. Thus, our data establish two pivotal roles for MEICA1 in meiosis: preventing aberrant meiotic recombination and regulating crossover formation.