The invention relates to a method of judging the thermostability of a protein, comprising the steps of calculating an analytical value specific to a test protein by a principal component analysis based on the amino acid composition of the protein calculated from the data of the amino acid sequence of the protein or the nucleotide sequence of the gene and comparing the analytical value with an analytical value of a protein which is retained by a thermostable organism and corresponds to the test protein, and further relates to a program for allowing a computer to execute processing for judging the thermostability of a protein by the method, and a computer readable recording medium having recorded the program thereon.