Quantum measurements based on mutually unbiased bases (MUB) play crucial roles in foundational studies and quantum information processing. It is known that there exist inequivalent MUB, but little is known about their operational distinctions, not to say experimental demonstration. In this work, by virtue of a simple estimation problem we experimentally demonstrate the operational distinctions between inequivalent triples of MUB in dimension 4 based on high-precision photonic systems. The experimental estimation fidelities coincide well with the theoretical predictions with only 0.16$\%$ average deviation, which is 25 times less than the difference (4.1$\%$) between the maximum estimation fidelity and the minimum estimation fidelity. Our experiments clearly demonstrate that inequivalent MUB have different information extraction capabilities and different merits for quantum information processing.
