Can I disable the watchdog timer for this specified function (which must not be disabled but just for testing purpose)? It is possible to use more timeOut for the watchdog on that specified function?
Let's forget that one - it is a really bad idea. If it is possible to defeat the watchdog, then it is possible to do it by error, and then the whole point of the watchdog is defeated. Apart from that its an XY question - a question about your proposed solution to a different problem - you should ask about the problem directly.
Must I develop another task with a big delay in other to run the algorithm? But the problem is that the algorithm need to be synchronised with the 1ms task since we are receiving CAN commands.
Yes you need another task, but you should not add a "big delay" and it is probably unnecessary and certainly a bad design. If the 1ms task needs the result of the algorithm then, the algorithm should run in a service task triggered by the 1ms task and run asynchronously to the 1ms task, the service task then makes the results available to the 1ms task when available (by shared memory or message passing perhaps). Alternatively if the result is not specifically needed by the 1ms task, the service task could take the necessary action independently of the 1ms task.
There are many options, but essentially it seems that your task partitioning is inappropriate; your CAN Rx task should be responsible for receiving CAN messages only, and any action required in response to CAN messages deferred to one or more other tasks, perhaps fed from a message queue.
What are other options to try ?
Software design should not be a matter of trial and error - get the design right, implement the design. However you might consider whether 1ms is appropriate; is it possible that the period can be extended to encompass the worst case execution time without causing a failure to meet deadlines in general? If the answer is "no" then the algorithm does not belong in this task.