Abstract: The North Equatorial Countercurrent (NECC) exhibits significant interannual variation, drastically affecting the global climate. This study compared the simulation results of the high-resolution model FGOALS-f3-H and the low-resolution model FGOALS-f3-L, both part of the flexible global ocean–atmosphere–land system model (FGOALS) climate system. The simulations, combined with Simple Ocean Data Assimilation (SODA) assimilation data, examine NECC’s average climate state, interannual variation characteristics, and its specific relationship with El Niño Southern Oscillation (ENSO) from 1994 to 2014. The study compared and analyzed the simulated and observed interannual changes in the NECC, specifically examining wind stress zonal transport, flow axis location, and NECC’s movement within the range of 0°–10°N. The ocean model of FGOALS-f3-H, with a horizontal resolution of approximately 10 km, effectively simulates the NECC’s strength, location, and connection with the New Guinea Coastal Current and Mindanao Current, two low-latitude western boundary currents. However, the low-resolution model FGOALS-f3-L, with a horizontal resolution of approximately 100 km, shows biases in the NECC, such as weak intensity, wide width, weak interannual variations, and shallow depth. Additionally, the interannual variations of the NECC simulated by the two versions demonstrated significant differences. During El Niño years, the NECC simulated by FGOALS-f3-H moved toward the equator but with decreased strength, while FGOALS-f3-L shifted towards the equator with increased transport volume. Differences between the high- and low-resolution models are more pronounced near the equator (0°–3°N), where FGOALS-f3-L may simulate the NECC extending southward to the equator, unlike FGOALS-f3-H, which positions it primarily north of 2°N. In the range of 0°–3°N, both models exhibit a significant correlation in zonal transport, with correlation coefficients of 0.67 and 0.64, suggesting that wind stress curl is the primary factor influencing zonal transport in this region.