The soft (logical) reconfiguration mainly include re-programming of machines, re-scheduling, including re-planning, re-routing and increasing/decreasing of shifts or number of workers according to task changes. In order to solve multi-constrains and multi-objective flexible job-shop scheduling problem (FJSP), a multi-objective and real-time scheduling algorithm was presented based on resource configuration, task constrains and scheduling objectives. It overcomes the traditional difficulty to find optimal combined heuristic rules for multi-objective, meanwhile keeps the simpleness of the scheduling rules. Finally, Flexsim software modeling and simulation method was used to validate its feasibility and effectiveness. At the same time, resource configuration schemes were generated based on the presented algorithm and the optimal scheme was selected. The results obtained from the computational study have shown that the proposed algorithm is a viable and effective approach for the multi-objective FJSP