The growth trajectories of the fishes during their early developmental phase are not adequately understood due to the continuous changes in their morphology, behaviour, and feeding habits. Understanding these interactions in relation to the habits, habitat, rate of growth, rate of development, and duration of different stages of growth are useful in predicting the direction of ecological and evolutionary changes in the life history of fishes. Using, geometric morphometric methods, we investigated the stage-specific phenotypic plasticity of Dascyllus carneus (cloudy damsel) in captivity during the entire larval development and metamorphosis. Each developmental stage has its unique shape and size, showing significant phenotypic plasticity (p < 0.001). The allometric analysis showed that D. carneus did not change its linear pattern of allometric growth trajectory till the stage of postflexion. In contrast, non-allometric growth analysis indicated a sudden shift from negative to positive allometric growth after the postflexion stage. Based on the results, it can be concluded that both in allometric and non-allometric analyses, except the yolk sac stage, all the other post-embryonic stages followed allometric growth patterns. Apart from the stage- specific phenotypic plasticity, the similarity and dissimilarity of each developmental stage were validated using statistical methods, such as discriminant function analysis (DFA), two-block partial least square (2B-PLS), and canonical variate analysis (CVA). All stages were seen distributed into a unique trait-based morphospace as each stage contained unique shape and size features. In our study, 2B-PLS was used to unveil the head and trunk integration at each stage. We establish that, the development of head and trunk are in separate morphological modules after the yolk sac and preflexion stages. From the overall analyses, all stages, except the juvenile stage, were observed to show high level of heterogeneity and at the transition stage, well-adapted individuals were observed. Stage-specific analysis and understanding of stage-specific requirements of developing larvae will help to surpass some challenges in larval rearing practices, which are discussed in this paper.