The performance of different height models (BSE-1979, AMTB-2013, and SHU-2015) in the International Reference Ionosphere (IRI-2016) is evaluated over the Indian equatorial and low latitude sectors. The impact of deviations in the modelled hmF2 on the estimation of electron density profiles and the Total Electron Content (TEC) is examined using the three different hmF2 methods in IRI-2016. For this study digisonde observations over Trivandrum (8.5 °N, 76.9 °E) and Ahmedabad (23.0 °N, 72.5 °E) along with GPS observations over Colombo (6.8 °N, 79.8 °E) and Ahmedabad during a high solar activity year 2014 are considered. A comparison of electron density profiles between digisonde and IRI-2016 at both the equatorial station, Trivandrum, and the low latitude station, Ahmedabad, revealed significant deviations with higher deviations in the post sunset hours at the equator. The three height methods have shown significant differences in their predictions of hmF2 at both locations. At the equator, the SHU-2015 method shows better estimates closer to the measurement values, than the other two methods except at Pre-Reversal Enhancement (PRE) time, during which, the AMTB-2013 method shows better performance. At the low latitude station, the newly added methods (SHU-2015 and AMTB-2013) do not indicate any improvements in estimating the hmF2. The availability of three different height methods in IRI-2016 is exploited to understand the modifications if any, in the ionospheric height structure and TEC for different hmF2 methods and the corresponding results are presented. As the variations in hmF2 are used to derive vertical drift on many occasions in the absence of incoherent scatter radar, this study is significant in assessing the relative efficacy of the three height models and hence useful to understand various ionospheric processes over the low/equatorial latitudes.