Key message Using in silico experiment in crop model, we identified different physiological regulations of yield and yield stability, as well as quantify the genotype and environment numbers required for analysing yield stability convincingly. Abstract Identifying target traits for breeding stable and high-yielded cultivars simultaneously is difficult due to limited knowledge of physiological mechanisms behind yield stability. Besides, there is no consensus about the adequacy of a stability index (SI) and the minimal number of environments and genotypes required for evaluating yield stability. We studied this question using the crop model APSIM-Wheat to simulate 9100 virtual genotypes grown under 9000 environments. By analysing the simulated data, we showed that the shape of phenotype distributions affected the correlation between SI and mean yield and the genotypic superiority measure ( P i ) was least affected among 11 SI. P i was used as index to demonstrate that more than 150 environments were required to estimate yield stability of a genotype convincingly and more than 1000 genotypes were necessary to evaluate the contribution of a physiological parameter to yield stability. Network analyses suggested that a physiological parameter contributed preferentially to yield or P i . For example, soil water absorption efficiency and potential grain filling rate explained better the variations in yield than in P i ; while light extinction coefficient and radiation use efficiency were more correlated with P i than with yield. The high number of genotypes and environments required for studying P i highlight the necessity and potential of in silico experiments to better understand the mechanisms behind yield stability.