We propose a boundary scheme for addressing multi-mechanism flow in a porous medium in slip and early transition flow regimes, which is frequently encountered in shale gas reservoirs. Micro-gaseous flow in organic-rich shale involves a complex flow mechanism. A self-developed boundary scheme that combines the non-equilibrium extrapolation scheme and the combined diffusive reflection and bounce-back scheme (half-way DBB) to embed the Langmuir slip boundary into the single-relaxation-time lattice Boltzmann method (SRT-LBM) enables us to describe this process, namely, the coupling effect of micro-gaseous flow and surface diffusion in organic-rich nanoscale pores. The present LBM model comes with the careful consideration of the local Knudsen number, local pressure gradient, viscosity correction model, and regularization procedure to account for the rarefied gas flows in irregular pores. Its validity and accuracy are verified by several benchmarking cases, and the calculated results by this boundary scheme accord well with our analytical solutions. This boundary scheme shows a higher accuracy than the existing studies. Additionally, a subiteration strategy is presented to tackle the coupled micro-gaseous flow and surface diffusion, which necessitates the iteration process matching of these two mechanisms. The multi-mechanism flow in the self-developed irregular pores is also numerically investigated and analyzed over a wide range of parameters. The results indicate that the present model can effectively capture the coupling effect of micro-gaseous flow and surface diffusion in a tree-like porous medium.