An analog-to-digital converter (ADC) system includes a main ADC, a reference ADC, a sampling control circuit, and a calibration circuit. The main ADC obtains a first sampled input voltage by sampling an analog input according to a first sampling clock, and performs analog-to-digital conversion upon the first sampled voltage to generate a first sample value. The reference ADC obtains a second sampled voltage by sampling the analog input according to a second sampling clock, and performs analog-to-digital conversion upon the second sampled voltage to generate a second sample value. The sampling control circuit controls the second sampling clock to ensure that the second sampling clock and the first sampling clock have a same frequency but different phases, and adjusts the second sample value to generate a reference sample value. The calibration circuit applies calibration to the main ADC according to the first sample value and the reference sample value.