We performed microsecond-long, atomistic molecular dynamics simulations on a series of precise poly(ethylene-co-acrylic acid) ionomers neutralized with lithium, with three different spacer lengths between acid groups on the ionomers and at two temperatures. Ionic aggregates form in these systems with a variety of shapes ranging from isolated aggregates to percolated aggregates. At the lower temperature of 423 K, the ionic aggregate morphologies do not reach a steady-state distribution over the course of the simulations. At the higher temperature of 600 K, the aggregates are sufficiently mobile that they rearrange and reach steady state after hundreds of nanoseconds. For systems that are 100% neutralized with lithium, the ions form percolated aggregates that span the simulation box in three directions, for all three spacer lengths (9, 15, and 21). In the partially neutralized systems, the morphology includes lithium ion aggregates that may also include some unneutralized acid groups, along with a coexisting population of acid group aggregates that form through hydrogen bonding. In the lithium ion aggregates, unneutralized acid groups tend to be found on the ends or sides of the aggregates.