In this article, we study the multiroute job shop scheduling problem with continuous-limited output buffers (MRJSP-CLOBs). In contrast to the standard job shop scheduling problem (JSP), continuous-limited output buffers render the commonly used graph-based approaches inapplicable, and the multiroute issue further increases computational complexity. To this end, we formulate MRJSP-CLOB as a mixed-integer linear program (MILP), which is typically NP-hard. Then, we extend the critical block in the JSP by utilizing the no-time-gap relationship and design a new neighborhood structure. Furthermore, we propose a hybrid artificial immune-simulated annealing algorithm (AIA-SA) by sharing iterations and integrating a random infeasible solution repairing algorithm with a new SA acceptance rule, which enables individuals to share information and increases the robustness of the corresponding SA parameters. Finally, the AIA-SA is compared with CPLEX and state-of-the-art algorithms on MRJSP-CLOB with different sizes. Experiments for large-sized instances demonstrate that our algorithm requires less than 3% computing time of the CPLEX, while being faster and more accurate than the other algorithms.