Abstract Quantum algorithms offer enhanced computational efficiency compared to their classical counterparts in solving specific tasks. In this study, we implement the quantum permutation algorithm utilizing a polar molecule within an external electric field. The selection of the molecular qutrit involves the utilization of field-dressed states generated through the pendular modes of SrO. Through the application of multi-target optimal control theory, we strategically design microwave pulses to execute logical operations, including Fourier transform, oracle Uf operation, and inverse Fourier transform within a three-level molecular qutrit structure. The observed high fidelity of our outcomes is intricately linked to the concept of the quantum speed limit, which quantifies the maximum speed of quantum state manipulation. Subsequently, we design the optimized pulse sequence to successfully simulate the quantum permutation algorithm on a single SrO molecule, achieving remarkable fidelity. Consequently, a quantum circuit comprising a single qutrit suffices to determine permutation parity with just a single function evaluation. Therefore, our results indicate that the optimal control theory can be well applied to quantum computation of polar molecular systems.