Determining the number concentration of minor constituents in the atmosphere is very important as it determines the whole tropospheric chemistry process. These constituents may act as cloud condensation nuclei (CCN) and ice nuclei (IN), impacting heterogeneous nucleation inside the cloud. However, the estimations of the number concentration of CCN/IN in cloud microphysical parameters are associated with uncertainties. In the present work, a hybrid Monte Carlo Gear solver has been developed to retrieve profiles of CH4, N2O, and SO2. The idealized experiments have been carried out using this solver for retrieving vertical profiles of these constituents over four megacities, viz., Delhi, Mumbai, Chennai, and Kolkata. Community Long-term Infrared Microwave Coupled Atmospheric Product System (CLIMCAPS) dataset around 0800 UTC (2000UTC) has been used for initializing the number concentration of CH4, N2O, and SO2 for daytime (nighttime). The daytime (nighttime) retrieved profiles have been validated using 2000 UTC (next day 0800 UTC) CLIMCAPS products. ERA5 temperature dataset has been used to estimate the kinematic rate of reactions with 1000 perturbations determined using Maximum Likelihood Estimation (MLE). The retrieved profiles and CLIMCAPS products are in very good agreement, as evidenced by the percentage difference between them within the range of 1.3 × 10−5–60.8 % and the coefficient of determination mainly within the range between 81 and 97 %. However, during the passage of tropical cyclone and western disturbance, its value became as low as 27 and 65 % over Chennai and Kolkata, respectively. The enactment of synoptic scale systems such as western disturbances, tropical cyclone Amphan, and easterly waves caused disturbed weather over these megacities—the retrieved profiles during disturbed weather cause large deviations of vertical profiles of N2O. However, the profiles of CH4 and SO2 have less deviation. It is inferred that incorporating this methodology in the dynamical model will be useful to simulate the realistic vertical profiles of the minor constituents in the atmosphere.