The association between atmospheric weather conditions along the equatorial electrojets and complexity in emergence flux in solar magnetic activity involved in the weather fluctuation processes may be substantial such that it affect the weather conditions particularly in the earth’s equatorial regions. In this study, we have analysed relevant parameters influencing the atmospheric weather conditions across the major cities and zones in Nigeria with solar magnetic activity and cosmic ray intensity covering five solar cycles from 19 to 24. Our investigation was principally based on solar magnetic activity which include solar parameters; flare index, cosmic ray, and atmospheric weather parameters including temperature, relative humidity, and precipitation. We utilized the cross-correlation and wavelet coherence techniques. The study found that the Northern region (Guinea and Sahel Savannah) located along 8.92 to 13.70 degrees latitudes and the Southern regions (Coastal and Derived) located within latitudes 4.5 and 8.9 degree latitudes responded differently to various atmospheric and solar parameters. The temperature and relative humidity in the northern parts is comparatively higher than in the southern region, while the southern region experienced higher precipitation. The flare index and cosmic ray exhibit different patterns as well negatively correlated. The relationships between the precipitations and relative humidity across Nigeria show a distinct behaviour which could be attributed to concentrations of ions influencing cloud properties across the country. There are strong and positive correlations between the two indices, with high coefficients specifically during the examined solar cycles. The difference in responses between Southern and Northern Nigeria could be attributed to mechanism driving the atmospheric weather through the Earth latitudinal couplings.