Respiratory sinus arrhythmia (RSA) is known as fluctuations of heart rate associated with breathing. It has been increasingly used as a noninvasive index of cardiac vagal tone in psychophysiological research recently. Its analysis is often influenced or distorted by respiratory parameters, posture and action, etc. This paper reviews five methods of quantification, including the root mean square of successive differences (RMSSD), peak valley RSA (pvRSA), cosinor fitting, spectral analysis, and joint timing-frequency analysis (JTFA). Paced breathing, analysis of covariance, residua method and msRSA per liter tidal volume are adjustment strategies of measurement and analysis of RSA in this article as well. At last, some prospects of solutions of the problems of RSA research are given.