Soliton molecules (SMs), bounded and self-assembled of particle-like dissipative solitons, exist with versatile mutual interactions and manifest substantial potential in soliton communication and optical data storage. However, controllable manipulation of the bounded molecular patterns remains challenging, as reaching a specific operation regime in lasers generally involves adjusting multiple control parameters in connection with a wide range of accessible pulse dynamics. An evolutionary algorithm is implemented for intelligent control of SMs in a 2 μm ultrafast fiber laser mode locked through nonlinear polarization rotation. Depending on the specifications of the merit function used for the optimization procedure, various SM operations are obtained, including spectra shape programming and controllable deterministic switching of doublet and triplet SMs operating in stationary or pulsation states with reconfigurable temporal separations, frequency locking of pulsation SMs, doublet and SM complexes with controllable pulsation ratio, etc. Digital encoding is further demonstrated in this platform by employing the self-assembled characteristics of SMs. Our work opens up an avenue for active SM control beyond conventional telecom bands and brings useful insights into nonlinear science and applications.