Overexpression of Bcl-2, a typical anti-apoptotic protein, is one of the most effective means to maintain mitochondria integrity in recombinant CHO (rCHO) cell culture treated with sodium butyrate (NaBu). NaBu is known as a typical specific productivity-enhancing factor and also a well-known apoptosis inducer. Bcl-2 is distributed to and functions in multiple intracellular organelles such as the nucleus, mitochondria, and endoplasmic reticulum (ER). To evaluate the effect of organelle-specific overexpression of Bcl-2 on NaBu-induced apoptosis in rCHO cells, Bcl-2 expression was restricted to the mitochondria or to the ER either by employing a mitochondrial insertion sequence of ActA or by insertion of an ER-specific sequence of cytochrome b5 to their respective sequences. The rCHO cell lines overexpressing wild-type Bcl-2 (WT-Bcl-2), mitochondrial Bcl-2 (MT-Bcl-2), and ER-targeted Bcl-2 (ER-Bcl-2) were established. Overexpression of WT-Bcl-2, MT-Bcl-2, and ER-Bcl-2 could increase cell viability and decrease LDH release under NaBu-treated conditions. Additionally, overexpression of WT-Bcl-2, MT-Bcl-2, and ER-Bcl-2 could suppress NaBu-induced apoptosis, as demonstrated by a DNA fragmentation assay. A mitochondrial membrane potential assay revealed that ER-Bcl-2 overexpression can maintain the mitochondrial membrane integrity without being affected by MT-Bcl-2 overexpression, indicating that the role of ER should be considered in alleviating NaBu-induced apoptosis by a genetic modulation strategy. Taken together, it was found that restricted Bcl-2 overexpression at the ER can inhibit the NaBu-induced apoptosis by maintaining mitochondria integrity in rCHO cells.