The invention relates to an isotope based surface water pollution source analytical method, which comprises the steps of: 1) sampling: laying sampling points and conducting sampling according to industry standards; 2) isotope detection: taking isotopes of hydrogen, oxygen, carbon and nitrogen, namely D, <18>O, <13>C, and <15>N as the indexes; employing an isotope ratio mass spectrometer to detect the ratios of isotopes of hydrogen, oxygen, carbon and nitrogen, namely D, <18>O, <13>C, and <15>N in samples, and conducting comparison with international standard substances, and working out isotope ratios of the samples; and 3) data analysis: drawing a hydrogen and oxygen isotope ratio diagram according to the ratios of isotopes of hydrogen and oxygen, namely D and <18>O in source and convergence samples; selecting analysis nodes, calculating a pollution source contribution rate through a source convergence isotope ratio of the nodes, and determining a new pollution source by judging whether the source convergence isotope ratio of outflow nodes is balanced, and then making use of analysis of the isotopes of carbon and nitrogen, namely <13>C and <15>N to verify the accuracy of the result. The method provided by the invention has the advantages of improving the accuracy and efficiency.