This invention provides a process for producing an isotope-labeled protein used as a sample for protein 3D structural analysis via NMR in a cost-effective manner within a short period of time. In this process, a protein is synthesized using, as a substrate, an amino acid mixture that contains a maximum of 19 different types of amino acids selected from the group consisting of alanine, arginine, aspartic acid, cysteine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, asparagine, and glutamine in a cell-free protein synthesis system.