A moving-magnet type linear motor controlling system which can highly accurately control carts even when a plurality of coil units apply forces to the carts is provided. The moving-magnet type linear motor controlling system has: a plurality of coil units having a plurality of coils; a position detecting unit for detecting the positions of the plural carts which are moved along the plurality of coil units; and a controlling unit for determining a ratio of currents which are supplied to the plural coil units on the basis of the positions of the plural carts and an impedance and thrust characteristics of each of the plural coil units.