To increase the flexibility of the non-dimensional lattice Boltzmann method (NDLBM), a non-uniform stretched mesh scheme was developed for coupled flow and heat transfer simulations. Mesoscopic scale governing equations and parameters are obtained through coordinate transformation between the non-uniform and uniform mesh spaces. Different from conventional single relaxation time closure models of the collision process, which need space interpolations and momentum adjustments, the present collision model is related to transformed relaxation time and force matrixes. Additional interpolations and adjustments are not necessary because the effects of local grids and properties are included in each component of the matrixes. The components of the relaxation time matrixes are directly expressed by mesoscopic governing parameters, discrete directions and local stretch gradients. Natural convection in an enclosure is simulated with meshes of various global stretch ratios and grid numbers. The non-uniform stretched mesh scheme can capture the temperature and velocity distributions as well as Nusselt numbers with negligible deviations from the uniform grids. Deviations increase slightly with global stretched ratios and appear at larger local velocity and grid size positions. Effects of the tilt angle and key governing parameters from conduction to convection regimes are illustrated and compare favorably with previous studies.