To provide a heat source control system and heat source control method enabling operation of each control module by a common measurement item to achieve a stable control state and saving energy of carrying power, in a closed two-pump type heat source system.

The heat source system includes: a plurality of heat source machines; a plurality of primary pumps carrying heat source water; a going water primary header and a going water secondary header mixing the heat source water; a plurality of secondary pumps sending water from the going water primary header to the going water secondary header; an air conditioning load receiving supply of the heat source water from the secondary pumps; an air conditioner two-way valve on the outlet side of the air conditioning load; a return water header to which the heat source water is returned; and a communication pipe between the going water primary header and the going water secondary header. The communication pipe includes a control two-way valve, and a pressure sensor detecting the pressure of the going water primary header is provided. When the control two-way valve is closed with all air conditioner two-way valves fully closed, the control two-way valve is controlled by using the pressure immediately before error stop of the heat source machines due to decline in the flow rate as a pipe interior pressure target value of the going water primary header.