Lean-stratified water injection is one of the most important technologies to increase production and develop potentials for the oilfield with extreme high water content. However, traditional models cannot entirely solve the inner boundary conditions of lean-stratified water injection. Therefore, we established the injection wellbore constraint equations, which were coupled with the oil/water two-phase numerical reservoir models, and then the seven diagonal form sparse coefficient matrix was solved by block precondition of generalized minimal residual algorithm. Considering the specific situation of lean-stratified water injection wells, reservoir geology and production schemes of the middle part of the sixth Oilfield in Xing Shugang, three mechanism models of multi-layer heterogeneous reservoir were constructed to simulate the lean-stratified water injection. The influences of different segments numbers, modes of combination in segment layer and rhythm characteristics of remaining oil reserves and distribution are evaluated.