Modifications　to　the　alkyl　side　chains　of　Y6-type　nonfullerene　acceptors　(NFAs)　continuously　break　through　the　organic　solar　cells　(OSCs)　efficiency　by　enhancing　electron　mobility.　However,　the　role　of　side　chains　in　molecular　aggregation　and　charge　transport　across　different　aggregates　remains　unclear.　By　employing　a　multiscale　approach　in　combination　with　density　functional　theory　(DFT),　molecular　dynamics　(MD)　simulations,　and　kinetic　Monte　Carlo　(KMC),　we　addressed　the　issue　of　how　side　chains　impact　molecular　aggregation,　energy　disorder,　and　the　formation　of　near-macroscopic　(∼0.3 µm)　conductive　network,　which　are　critical　for　boosting　electron　mobility.　Specifically,　the　side-chain　structure　greatly　influences　the　un-conjugated　enveloping　effect　on　backbones　within　aggregates.　The　effect　diminishes　with　longer　linear　side　chains　and　is　further　minimized　by　using　branched　side　chains.　Though　static　energy　disorder　increased,　the　improved　connectivity　of　the　conductive　network　led　to　a　notable　increase　in　electron　mobility　(from　2.4 × 10−4　to　3.9 × 10−4　cm2·V−1·s−1).　The　findings　offer　insight　into　controlling　molecular　aggregation　via　alkyl　side　chains,　which　helps　to　further　unlock　the　potential　of　Y6-type　NFAs.　©　2024　The　Author(s).　Aggregate　published　by　SCUT,　AIEI　and　John　Wiley　&　Sons　Australia,　Ltd.