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Aiming at the Hadoop heterogeneous computer clusters that have the defects of low scheduling efficiency for in-conformal computing and data resource, a job scheduling method based on Late algorithm based on Hadoop computer cluster was proposed. Firstly, the principle of scheduling based on Hadoop and Map-Reduce model was introduced, then on the basis of the classic scheduling algorithm, the executing time ratio for stages of Map task and Reduce task was stored and renewed, In order to improve the scheduling efficiency further, the slow task is transferred to the local node or the neighbor nodes near the data resource, and the algorism flow for the improved Late algorism was given. In order to verify the method in this paper, the experiment was simulated in the Hadoop computer cluster, the number for Jobtracker nodes and Tasktracker number is 1 and 7, respectively, and the result shows the method in this paper can realize job scheduling for heterogeneous computer clusters, and compared with the other method, it has the low predicating error and high scheduling efficiency.