There are provided an analyzing system and a control method thereof which are capable of preventing a discrepancy from arising between a condition set by using a condition setting device and a condition set by using an operation section of each unit. Setting of a condition using the operation section is restricted at each unit controlled by a control device at least when transmission/reception of data is being performed between the condition setting device and the control device. Accordingly, a different condition is not set by using the operation section of each unit when data of a condition set by using the condition setting device is transmitted to the control device. Thus, a discrepancy may be prevented from arising between the condition set by using the condition setting device and a condition set by using the operation section of each unit.