Biomolecular condensation is a pivotal mechanism in chromatin organization and nuclear compartmentalization. However, the molecular mechanism that drives heterochromatin organization and selectively partitions heterochromatin components in muscle cells remains unclear. Furthermore, its pathological implications remain unexplored. Here, we demonstrate that ChRO1, a muscle-specific RNA enriched with simple dinucleotide repeats, is associated with static heterochromatin foci containing similar repetitive elements in mouse muscle cells. Through its CU-repeat-rich region, ChRO1 promotes heterochromatin clustering and facilitates the selective partitioning of heterochromatin proteins, as shown in vitro and in C2C12 cells. Consequently, chromatin interaction stabilized at ChRO1-bound regions, reinforcing TAD boundaries and promoting inactive chromatin states. The enhanced intra- and interchromosomal interactions secure the heterochromatinization of non-muscle genes, highlighting ChRO1's role in chromatin organization. Disruption of ChRO1 or perturbation of condensate organization induces chromocenter disintegration and muscle atrophic phenotypes, underscoring the importance of these processes in maintaining muscle integrity. Notably, ChRO1 mitigates chromocenter disintegration and atrophic phenotypes in chemically induced atrophy models, emphasizing its protective role. These findings reveal a novel repeat-rich RNA-based mechanism of repetitive DNA condensation that safeguards heterochromatin organization and muscle integrity, providing mechanistic insight and therapeutic implications for muscle-related disorders.