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The deterministic simple least square (LS) approach is employed in the covariance analysis of the total neutron cross section (n,tot) calculated by a microscopic optical potential, CTOM, which is based on a fundamental theory − Dirac Brueckner Hartree Fock. The sensitivity to the CTOM parameters is firstly systematically calculated for 77 stable nuclei in the range 12C–208Pb within neutron energy 5–200 MeV. Then, an equivalent covariance of experimental data (EVexp) is constructed to describe the experimental data uncertainties and the systematic difference between experimental data and CTOM calculation. The variance and covariance of EVexp matrix are both evaluated via the Gaussian analysis to the ratios of measured (n,tot) cross sections and the CTOM calculations. In addition, a technique named “selection of effective points (SEP)” is suggested additionally to reduce the influence of the Peelle's Pertinent Puzzle problem in this work.