With the rapid increment of the heterogeneity of hardware devices, cluster computing has to encounter the problem of handling heterogeneous resources for exploiting the utilization of system resources. This paper introduces a new job allocation strategy based on multi-clusters in diskless environments. By adopting Ganglia as the resource monitor and Condor as the queue system, a heterogeneous multi-cluster system is also constructed with and without storage devices for evaluating the system performance. The proposed algorithm is called the Well-Balanced Allocation Strategy (WBAS) in which the scheduler dispatches MPI-based jobs to appropriate resources across multi-clusters. The strategy focuses on dispatching jobs to nodes with similar performance, thus equalizing execution times among all the required nodes. The WBAS is implemented on the constructed heterogeneous multi-cluster system to evaluate the performance of the scheduling strategy. The experimental results show that the proposed strategy performs well and could efficiently improve the system performance.[