Glutaredoxins (Grxs) are small proteins that share a well‐conserved thioredoxin (Trx)‐fold and participate in many biological processes. This study examined the cold adaptation mechanism of a Fe‐S cluster binding class II Grx4 (SpGrx4) from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621. Three polar residues close to the cis‐proline residue (P73) of SpGrx4 form a hydrogen bond network (Q74–S67–Y76) with the cis‐proline loop main chain. The hydroxyl group of S67 or Y76 or both is replaced in similar Grxs depending on the temperature of the habitat. Mutants with reduced hydrogen bonds (S67A, Q74A, Y76F, and S67A/Y76W) were more susceptible to urea‐induced unfolding and more flexible than the wild‐type (WT). By contrast, Y76W, with a bulky indole group, was the most stable. These mutants showed higher melting temperatures than WT as a consequence of increased hydrophobic interactions. These results suggest that the tyrosine residue, Y76, is preferred for the cold adaptation of SpGrx4 with a heat‐labile structure despite the rigid cis‐proline loop, due to hydrogen bond formation. An aromatic residue on β3 (cis‐proline plus3) modulates the stability‐flexibility of the cis‐proline loop for temperature adaptation of prokaryotic class II Grx4 members via hydrogen bonds and hydrophobic interactions.