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In this work, we propose a composite pulses scheme by modulating phases to achieve high fidelity population transfer in three-level systems. To circumvent the obstacle that not enough variables are exploited to eliminate the systematic errors in the transition probability, we put forward a cost function to find the optimal value. The cost function is independently constructed either in ensuring an accurate population of the target state, or in suppressing the population of the leakage state, or both of them. The results demonstrate that population transfer is implemented with high fidelity even when existing the deviations in the coupling coefficients. Furthermore, our composite pulses scheme can be extensible to arbitrarily long pulse sequences. As an example, we employ the composite pulses sequence for achieving the three-atom singlet state in an atom-cavity system with ultrahigh fidelity. The final singlet state shows robustness against deviations and is not seriously affected by waveform distortions. Also, the singlet state maintains a high fidelity under the decoherence environment.