In recent years, El Nio Modoki (a type of pseudo-El Nio) has been distinguished as a unique large-scale ocean warming phenomenon happening in the central tropical Pacific that is quite different from the traditional El Nio. In this study, EOF analysis was used to successfully separate El Nio and El Nio Modoki. The abilities of the NINO3 index, NINO3.4 index, NINO1+2 index and NINO4 index in characterizing El Nio were explored in detail. The resulting suggestion was that, comparatively, NINO3 is the optimal index for monitoring El Nio among the four NINO indices, as the other NINO indices were found to be less good at distinguishing between El Nio and El Nio Modoki signals, or were easily disturbed by El Nio Modoki signals. Further, an improved El Nio Modoki index (IEMI) was introduced in the current paper to better represent the El Nio Modoki that is captured by the second leading EOF mode of monthly tropical Pacific sea surface temperature anomalies (SSTAs). The IEMI is an improvement of the El Nio Modoki index (EMI) through adjustments made to the inappropriate weight coefficients of the three boxes of EMI. The IEMI therefore overcomes the EMI’s inability to monitor the two historical El Nio Modoki events, as well as avoids the possible risk (present in the EMI) of excluding the interference of the El Nio signal. The realistic and potential advantages of the IEMI are clear.