The study delves into the epidemiological transition, examining the intricate changes in health status patterns and their connection to morbidities. Specifically, it assesses morbidity transition at both national and subnational levels in India and their determinants from 1995 to 2018. This study examines self-reported morbidities in India by utilising four rounds of National Sample Survey Organisation (NSSO) data (52nd, 60th, 71st, and 75th) from 1995–2018. We estimated prevalence by conducting descriptive analysis on socio-demographic determinants and morbidities such as: Infectious and Communicable Diseases (In&CDs), Non-communicable diseases (NCDs), Disability and other diseases. Moreover, we employed pooled regression analysis to explore morbidity risk transitions over the past decades. The study revealed a steady upsurge in morbidity prevalence in India, doubling from 56 (per thousand) in 1995 to 106 in 2014. However, a considerable decline was observed in the most recent round in 2018 (79 per thousand). From 1995 to 2018, NCDs gained a prominent share in morbidity trends. Kerala in the southern region reported the highest rates, followed by states like Lakshadweep, Andhra Pradesh, Karnataka, West Bengal, Punjab, and others. Age, sex, residence, education, caste, religion, and wealth are pivotal factors in determining the severity of different disease burdens in different sections of the population in India. Over the study period (1995, 2004, 2014, and 2018), the odds of reported morbidities risk transition significantly increased over successive decades: 1.81 times in 2004 (95% CI: 1.78–1.84), 2.16 times in 2014 (95% CI: 2.12–2.2), and 1.44 times in 2018 (95% CI: 1.41–1.46), compared to 1995 (52nd round). The study reveals significant disparities in morbidity reporting across Indian states from 1995 to 2018, attributed to distinct demographic, social, and economic determinants. India continues to grapple with the dual burden of diseases, but the NCDs burden is mounting at a faster pace than CDs.