A control system of a switching voltage regulator includes an adjustable switched-capacitor conversion circuit, an error generator, and a controlling module. The adjustable switched-capacitor conversion circuit has a plurality of discrete conversion rates, and selects a corresponding conversion rate and outputs an output voltage according to a signal of the conversion rate. An error generator is connected to the adjustable switched-capacitor conversion circuit and compares the output voltage with an external reference voltage to obtain an error voltage. The controlling module is connected between the error generator and the adjustable switched-capacitor conversion circuit to store a plurality of control variable sets, and selects one of plurality of control variable sets according to the error voltage. Afterwards, the controlling module calculates to output the signal of the conversion rate and further adjust the output voltage according to the selected control variable sets.