Strengthening the cooperation，and realizing the functional complementation and continuous service of medical institutions at county and township levels between medical institutions at county and township levels are crucial to tiered medical services in rural areas. It proposed the payment by disease for services between county and township medical institutions. The aspects of disease type selection，continuous service path，and payment standard and distribution scheme are designed to analyze its potential effects from the aspects of institutional income，out of pocket expenses，and health insurance expenditure.