An innovative multi-workshop facility layout problem is developed and investigated in this paper, which involves the placement of a series of departments into several workshop floors, meanwhile the clearance bounds among departments are also considered. In addition, the internal and external logistics costs are taken into account, both constitute total material handling cost. In order to solve the problem, a mixed integer linear programming model is formulated with minimizing objective of material handling cost. The model proposed in this paper is also able to present the unequal-area facility layout problem and special multi-floor facility layout problem. Finally, several benchmark instances that match our problems are selected and solved using CPLEX software, and the best layouts of them are obtained.