Recently, Parallel Intrusion Detection (PID) becomes very popular and its procedure of the parallel processing is called a PID application (PIDA). This PIDA can be regarded as a Bag-of-Tasks (BoT) application, consisting of multiple tasks that can be processed in parallel. Given multiple PIDAs (i.e., BoT applications) to be handled, when the private cloud has insufficiently available resources to afford all tasks, some tasks have to be outsourced to public clouds with resource-used costs. The key challenge here is how to schedule tasks on hybrid clouds to minimize makespan given a limited budget. This problem can be formulated as an Integer Programming model, which is generally NP-Hard. Accordingly, in this paper, we construct an Iterated Local Search (ILS) algorithm, which employs an effective heuristic to obtain the initial task sequence and utilizes an insertion-neighbourhood-based local search method to explore better task sequences with lower makespans. A swap-based perturbation operator is adopted to avoid local optimum. With the objective of improving the proposal’s efficiency without loss of any effectiveness, to calculate task sequences’ objectives, we construct a Fast Task Assignment (FTA) method by integrating an existing Task Assignment (TA) method with an acceleration mechanism designed through theoretical analysis. Accordingly, the proposed ILS is named FILS. Experimental results show that FILS outperforms the existing best algorithm for the considered problem, considerably and significantly. More importantly, compared with TA, FTA achieves a 2.42x speedup, which verifies that the acceleration mechanism employed by FTA is able to remarkably improve the efficiency. Finally, impacts of key factors are also evaluated and analyzed, exhaustively.