For plants or crops exposed to salinity stress, chloride channels (CLCs) play crucial functions in the regulation of anion (such as Cl− and NO3−) absorption, transport and distribution or anion homeostasis. In this study, how the physiological functions and molecular mechanisms of GhCLC5/16 genes affect Cl− -salinity tolerance in two upland cotton cultivars (the salt-tolerant cv. Lu7619 and the salt-sensitive cv. Xin51) was investigated using transformations of the yeast Δgef1 mutant, soybean hairy-root, Arabidopsis atclc-b mutant, and virus-induced gene silencing (VIGS) cotton plants. The results showed that, the target GhCLC5/16 genes, with the higher NaCl-induced upregulation of expression in the roots of Lu7619 plants, could complement the Cl−-sensitive phenotype of the yeast Δgef1 mutant. Under NaCl stress, compared to empty vector (EV) plants, GhCLC5/16-overexpressed soybean hairy-root composite plants (hrGhCLC5/16-OE) displayed enhanced NaCl tolerance with superior growth, lower relative electrolytic leakage (REL) values and malondialdehyde (MDA) contents in roots and leaves. Compared to the atclc-b mutant, atclc-b-GhCLC5 and atclc-b-GhCLC16 Arabidopsis seedlings displayed improved NaCl tolerance with less reduced root length, higher leaf chlorophyll content, lower shoot MDA content and REL values. GhCLC5/16-VIGS cotton plants displayed mitigated salt damage with significantly higher plant height and fresh weight (FW) than that of EV plants. The enhanced NaCl tolerance or mitigated salt damage of these plants, even with the salt-tolerant cv. Lu7619 (characterized by high GhCLC5/16 expression in the roots, whole plants, or GhCLC5/16-silencing in the leaves), occurs because the plants can accumulate more Cl− in the roots under NaCl stress, reduce the transport and accumulation of Cl− to shoots (especially the leaves), simultaneously enhance the NO3− content in the shoots/leaves, and thus significantly decrease the Cl−/NO3− ratio in the shoots/leaves. Therefore, GhCLC5/16 genes may be crucial members of the GhCLC family that contribute to the varied tolerance to Cl−-salinity observed in different cotton cultivars. The results may provide new perspectives and valuable candidate gene resources for molecular breeding of chloride-salinity tolerance in cotton and other crops.