Potential evapotranspiration (PET) indicates if a cultivation area is suitable for planting. Currently, site-specific PET models that are based on large geographic regions are vulnerable to inaccurate predictions as a result of climate change and sudden changes in the environmental abiotic stressors that affect plant growth. For the aim of promoting the papaya Sinta F1 cultivar, the study optimized the standard Thornthwaite PET model by integrating three advanced physics-based metaheuristics and evolutionary computing, namely atom search (ASO), differential evolution (DE), and multiverse (MVO) optimizers. The PET value was optimized through minimization as a function of air temperature, light intensity, heat index, and extended heat index. As the PET value approaches 0, it indicates that there is more soil-water content that can be absorbed by plants. Based on the four cultivation treatments (uncontrolled, ASO, DE, and MVO) exposed in three replicates within 90 days, the ASO-optimized Thornthwaite PET-treated (ASOTh) papaya plants resulted in the highest chlorophyll a and b concentrations, densest stomatal density, concentrated root and stem xylem and phloem vessels, considerable root and stem length, most formed leaf count, and strongest action potentials coming from stem membrane for both light and dark periods. This proves the applicability of the intelligent process in modifying the Thornthwaite model for plant growth promotion. Also, through the developed ASOTh, the stem length and thickness ratio was improved for mechanical stability to facilitate more branching leaves and potential fruits during the fruiting stage, and the chlorophyll a and b ratio was enhanced, which naturally extended the light energy band for photosynthesis. Overall, the newly developed ASOTh model may be used to grow papaya seedlings year-round anywhere on Earth if there is a control system to regulate the environmental setting inside the growth chamber.