Which transformer model are you using?
Most transformer models have the following convention as described in the component help: "A two-element vector containing the leakage inductance of the primary side L1 and the secondary side L2. The inductivity is given in henries (H)."
Both inductances are referred to their respective windings.
If still unclear, you can right-click the component and select Subsystem + Look under mask to see the underlying implementation of the component.