The latest delay chain-based FPGA TDCs can achieve resolutions around 10 ps. At such high levels of accuracy, delay chains become very sensitive to parasitic electromagnetic perturbations, including power supply voltage, temperature, and current surge. This paper describes how common-mode fast perturbation can deteriorate the spectra and make the root mean square (RMS) periodical as the input time interval increases. Based on this observation, an on-chip real-time correction method can be implemented, giving a correcting reference for each sample. Results show a typical RMS of 20 ps, with a maximum value below 30 ps, under the perturbation of around 100 mV and 20 kHz coming from the DC-DC module.