The invention provides a diatomite filtering machine unit for filtering collagen and a control method thereof. The diatomite filtering machine unit comprises a collagen liquid tank, a diatomite liquidtank, a first diatomite filtering machine and a second diatomite filtering machine which are connected through a plurality of valves and pipelines. The control method of the diatomite filtering machine unit comprises a first mode of using the first diatomite filtering machine as the standby machine and performing production by the second diatomite filtering machine, a second mode of using the second diatomite filtering machine as the standby machine and using the first diatomite filtering machine for production, and a third mode of using the two diatomite filtering machines for simultaneous production. The two diatomite filtering machines can realize one standby machine and one running machine; the problems of diatomite coating spreading and coating and waiting during the diatomite filtering machine repair can be solved; the production continuity is ensured; meanwhile, the two diatomite filtering machines can be used in a parallel connection way; the filtering quantity in the unit time is increased, so that different production requirements can be met; good practicability are realized.