Post-annealing effects on the crystal structure and superconductivity of the lithium- and hexamethylenediamine (HMDA)-intercalated superconductor Lix(C6H16N2)yFe2-zSe2 have been investigated. Through the post-annealing, a two-step reduction of the interlayer spacing between neighboring Fe layers, d, has been observed. It has been found that a new phase of Lix(C6H16N2)yFe2-zSe2 with d = 10.30(2)Å and Tc = 41K different from the as-intercalated phase is stabilized owing to the possible stable inclination of HMDA intercalated between FeSe layers. This result supports the domic relation between Tc and d in the FeSe-based intercalation superconductors. The reason why Tc increases with a decrease in d through the post-annealing is discussed.