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The behavior of molecules and molecular chains confined in 1D nanochannels imposed by external interactions is a problem of fundamental interest. Here, we report structural manipulation of iodine confined inside zeolite (AFI) nanochannels by the application of high pressure. Structural transformations of the confined iodine under pressure have been unambiguously identified by polarized Raman spectroscopy combined with theoretical simulation. The length of the iodine chains and the orientation and intermolecular interaction of the confined iodine have been tuned at the molecular level by applied pressure. Almost all the confined iodine can be tuned into an axially oriented state upon compression, favoring the formation of long chains. The long iodine chains can be preserved to ambient pressure when released from intermediate pressures.