A method of handling a multi-panel SS block transmission comprises the instructions of the BS transmitting a configuration set to the communication device, wherein the configuration set comprises a plurality of panel configurations; the BS configuring a primary panel with a primary SS block time index set and a primary time index order according to a first panel configuration; the BS configuring at least one secondary panel with at least one secondary SS block time index set and at least one secondary time index order according to at least one second panel configuration; the BS configuring the primary panel with a first association between a first beam index and a primary SS block time index; and the BS configuring the at least one secondary panel with at least one second association between at least one second beam index and at least one secondary SS block time index.