Ground-based GNSS (Global Navigation Satellite System) reference stations lack the capacity to provide data for ocean regions with sufficient spatial-temporal resolution, limiting the detailed study of the equatorial ionization anomaly (EIA). Thus, this study collected kinematic multi-GNSS data on the ionospheric Total Electron Content (TEC) during two research cruises across the equator in the Western Pacific Ocean in 2014 (31 October–8 November) and 2015 (29 March–6 April). The purpose of the study was to use sufficient spatial–temporal resolution data to conduct a detailed analysis of the diurnal variation of the equatorial ionization anomaly in different seasons. The two-year data collected were used to draw the following conclusions. During the test in 2014, the EIA phenomenon in the Northern and Southern Hemispheres was relatively obvious. The maximum values occurred at local time (LT) 15:00 (~136TECu) and LT22:00 (~107TECu) in the Northern Hemisphere and at LT14:00 (100TECu) and LT22:00 (80TECu) in the Southern Hemisphere. During the test in 2015, the EIA in the Southern Hemisphere reached its maximum level at LT14:00 (~115TECu) and LT20:00 (~85TECu). However, the EIA phenomenon in the Northern Hemisphere was weakened, and a maximum value occurred only at LT 15:00 (~85TECu). The intensity contrast was reversed. The EIA phenomenon manifests a strong hemisphere asymmetry in this region.