Abstract Quantum computing poses a significant threat to modern cryptosystems, prompting nations to initiate the development of next-generation cryptographic algorithms where quantum security assessment constitutes a critical task. In this work, we present the first complete quantum attack circuit construction and security evaluation of quantum resistance for the authenticated encryption algorithm MK-3, which features 16-bit S-boxes. Firstly, we achieve breakthroughs in finite field arithmetic. The arrangement method of Toffoli gates in the subfield $$F_{2^4}$$ F 2 4 enables two types of optimized $$F_{2^8}$$ F 2 8 multiplication circuits to reduce DW-cost by at least 50%. For $$F_{2^8}$$ F 2 8 inversion, by proposing a new intermediate state uncomputing technique, the DW-cost of the inversion circuit is reduced by at least 40% compared with existing solutions. This can also be used to optimize the quantum circuits of block ciphers such as AES and SM4. Secondly, we propose three types of quantum circuits for MK-3’s 16-bit S-box. The basic circuit reduces multiplicative bit operations to 115, representing at least 20% reduction. We propose a more compact S-box structure, reducing the number of circuit qubits for two types of S-boxes from 52 to 40. Finally, we implement full-algorithm quantum attacks and conduct security evaluations for MK-3. Complete quantum circuits supporting 128-bit and 256-bit keys are constructed, enabling Grover key search attacks. Security assessments confirm the 128-bit version meets NIST Security Category 1 (with reasonable inference of achieving Category 2), while the 256-bit version satisfies the highest Category 5 standards, demonstrating resistance against large-scale quantum computing attacks. This work achieves the first quantum circuit implementation for 16-bit S-boxes and provides critical evaluation benchmarks for post-quantum cryptography standardization.