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This paper addresses the complex job shop scheduling problem with the consideration of non-identical job sizes. By simultaneously considering practical constraints of sequence dependent setup times, incompatible job families and job dependent batch processing time, we formulate this problem into a simulation optimization problem based on the disjunctive graph representation. In order to find scheduling policies that minimise the expectation of mean weighted tardiness, we propose a genetic programming based hyper heuristic to generate efficient dispatching rules. And then, based on the nested partition framework together with the optimal computing budget allocation technique, a hybrid rule selection algorithm is proposed for searching machine group specified rule combinations. Numerical results show that the proposed algorithms outperform benchmark algorithms in both solution quality and robustness.