Controllable single‐molecule logic operations will enable development of reliable ultra‐minimalistic circuit elements for high‐density computing but require stable currents from multiple orthogonal inputs in molecular junctions. Utilizing the two unique adjacent conductive molecular orbitals (MOs) of gated Au/S‐(CH2)3‐Fc‐(CH2)9‐S/Au (Fc = ferrocene) single‐electron transistors (≈2 nm), a stable single‐electron logic calculator (SELC) is presented, which allows real‐time modulation of output current as a function of orthogonal input bias (Vb) and gate (Vg) voltages. Reliable and low‐voltage (ǀVbǀ ≤ 80 mV, ǀVgǀ ≤ 2 V) operations of the SELC depend upon the unambiguous association of current resonances with energy shifts of the MOs (which show an invariable, small energy separation of ≈100 meV) in response to the changes of voltages, which is confirmed by electron‐transport calculations. Stable multi‐logic operations based on the SELC modulated current conversions between the two resonances and Coulomb blockade regimes are demonstrated via the implementation of all universal 1‐input (YES/NOT/PASS_1/PASS_0) and 2‐input (AND/XOR/OR/NAND/NOR/INT/XNOR) logic gates.