The understanding of the atmospheric dynamics and thermodynamics in the time of climate change has become an unavoidable necessity for survival of humanity. We need to fill the research gaps with a more thorough and urgent research approach in the required domains. One of a major research gap whose filling could enrich our understanding of atmospheric dynamics and hydrological cycle is the vertical structure and distribution of cloud in atmosphere. Cloud vertical structure (CVS) significantly influences the quantity of solar radiation coming inside the atmosphere of Earth and thus it modulates the atmospheric adiabatic heating. It has also been found to be the major source of uncertainties in the global climate and weather models. In India the rural population is shifting to urbanized areas which are hub of intense economic activities and have high level of pollution. We witness high loading of anthropogenic aerosol in these highly urbanized areas which also varies seasonally. The association of these aerosols concentration with CVS has not been studied so far. Delhi is one of such large urban settlement and is also the most polluted Indian megacity. Therefore we have studied the CVS over Delhi using multi-year radiosonde and active satellite based data and also correlated it with aerosols concentration in the same region. The study includes a time series analysis of cloud base and top height with co-temporal and co-spatial AOD values for low-level, middle-level and high-level clouds. Significant trend in variation of cloud base and top height is found in our study. We have done the seasonal comparison of aerosols concentration with the CVS. And the study is showing that aerosols are influencing the CVS to a notable extent. The cloud vertical structure and aerosols also significantly influences the atmospheric temperature and the precipitation pattern and thus the hydrological cycle .Therefore, the effect of aerosol on clouds vertical structure in these polluted megacities could be very helpful for future climate projection and for understanding the hydrological cycle in these areas.