A naphthalimide-based fluorescent probe, Nap-I, with iodoacetamide as the alkylating group, has been synthesized, and its specific fluorescent staining of proteins containing cysteine (Cys) and selenocysteine (Sec) residues in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) has been evaluated. This molecule shows good fluorescence properties in the labeling of protein Cys/Sec residues, while reducing steric hindrance and minimizing changes in the water solubility of proteins. Reaction parameters, such as labeling time and pH, have been investigated, and the optimal labeling conditions for Cys-containing proteins have been determined. Thioredoxin reductase (TXNRD) is best stained at low pH. The probe Nap-I has been successfully used for the quantification of serum proteins and hemoglobin in Tan sheep serum, and TXNRD in Tan sheep liver and muscle has been labeled at low pH. Based on the probe Nap-I, we have also distinguished TXNRD1 and TXNRD2 by SDS-PAGE. The results showed that, compared with the normal microenvironment in which the protein resides, the lower the pH value, the greater the TXNRD activity.