Although great progress has been achieved in characterizing genetic constitutions of yield component traits in elite hybrids based on the traits at final harvest, there is still a major gap in the understanding on the biological mechanism as to how heterosis is generated. Long term observation in field performance of various crop hybrids indicates that heterosis is a dynamic process manifested throughout the life cycle. Recent development in phenomic platform has facilitated observation and measuring of dynamic performance of the plants. We used a high-throughput phenomic approach to obtain multiple i-traits to measure the biomass performance of 356 rice hybrids (many of them have been widely grown) and their parents in the whole life cycle. We found strong growth complementarity between the parental growth patterns in heterotic hybrids as measured using physiological ages of growth and development; in general parent one exhibits fast early growth but weak late growth while parent two relays strong late and reproductive growth, thus the hybrid combines the superiority from both parents to achieve heterotic performance throughout. We showed that the degree of ontogenetic complementarity between parents is highly associated with the amount of heterosis. We employed SY63, the most popular and well-studied rice hybrid, as a model to investigate genetic-genomic basis and the underlying genes of the ontogenetic complementarity using two large F2 populations. We identified 6-8 heterotic loci, including their main and digenic interaction effects, that may be sufficient to reconstruct the dynamic heterotic performance of SY63. These results suggest that complementarity of the parental genetic contributions at different developmental stages may be the major mechanism for the heterotic performance of hybrids. These findings may have significant implications for designed hybrid crop breeding.