the query can timeout if it is unable to acquire the required locks and resources. Every application needs timeot to prevent a query from running indefinelty. The Job might run for as long as needed but the queries within the job can still timeout if sql sees it as idle ( doing nothing)( if the query is actually performing work then it can continue to run for hours but idle state is acceptable only for few minutes.

try changing the logic to perform operations in batchs. Check where the timeout occure , tempdb , lock , block or deadclock? see if the right indexes are in place