The performance of second-order conditional moment closure (CMC) depends on models to evaluate conditional variances and covariances of temperature and species mass fractions. In this paper the closure schemes based on the steady laminar flamelet model (SLFM) are validated against direct numerical simulation (DNS) involving extinction and ignition. Scaling is performed to reproduce proper absolute magnitudes, irrespective of the origin of mismatch between local flamelet structures and scalar dissipation rates. DNS based on the pseudospectral method is carried out to study hydrogen–air combustion with a detailed kinetic mechanism, in homogeneous, isotropic, and decaying turbulent media. Lewis numbers are set equal to unity to avoid complication of differential diffusion. The SLFM-based closures for correlations among fluctuations of reaction rate, scalar dissipation rate, and species mass fractions show good comparison with DNS. The variance parameter in lognormal PDF and the constants in the dissipation term have been estimated from DNS results. Comparison is made for the resulting conditional profiles from DNS, first-order CMC, and second-order CMC with correction to the most critical reaction step according to sensitivity analysis. Overall good agreement ensures validity of the SLFM-based closures for modeling conditional variances and covariances in second-order CMC.