During the past three decades, the Caspian Sea (CS) ecosystem has undergone striking changes due to anthropogenic activities, particularly following the invasion of comb jelly Mnemiopsis leidyi that overfed on zooplankton in the late 1990 s. This study investigated the temporal and spatial patterns of the zooplankton community in CS over 25-year intervals using univariate and multivariate analyses. The objective was to assess the status of the zooplankton community through a comparison of the pre-invasion (1994–96) and post-invasion (2009–11 and 2018–19) of M. leidyi in the CS. The study revealed more zooplankton taxa for the pre-invasion period and fewer for the post-invasion period of 2018–19. Several key species such as Eurytemora grimmi, Polyphemus exicus, Synchaeta sp., and Calanipeda aquae dulcis disappeared post-invasion, and more than 50 taxa decreased to one-third in the post-invasion period. The abundance and diversity indices significantly declined following the invasion. The visualization of non-metric multidimensional scaling (nMDS) showed that periodic variations were more explanatory than assessments based on subareas and seasonal intervals. Significant differences were observed in the zooplankton assemblages across the three periods. In addition to highly affecting the zooplankton community, certain pelagic fish populations, notably those belonging to the kilka genus (Clupenella), have experienced significant decline as a result of M. leidyi invasion. In conclusion, the invasion of M. leidyi has caused major changes to the abundance and diversity of tropic levels in the CS, possibly through a combination of bottom-up and top-down forces at work in the ecosystem.