Poly(trimethylene terephthalate) (PTT) fibers have drawn much attention due to their excellent elastic recovery. Currently, PTT fibers with higher elasticity are in high demand in some special applications. In this article, in order to further improve the elasticity of PTT fibers, heat treatment with alternating tension and relaxation (AlterTR) was carried out, and as a comparison, heat treatments under the conditions of tension or relaxation were performed simultaneously. The relationships of conformation transition, crystallinity, and orientation with elastic recovery of heat treated PTT fibers were investigated. With the increase of crystallinity during the treatment, part of the higher-energy trans conformation of the heat treated PTT fibers was converted to a lower-energy gauche conformation, which is a primary cause of elastic recovery. AlterTR heat treated PTT fibers had both high crystallinity and high orientation, which resulted in a high elastic recovery of 79% at 30% fixed elongation after 5 cycles of stretching testing, 7% higher than untreated PTT fibers. The elastic recovery was also obviously higher than the PTT fibers heat treated under the conditions of tension or relaxation.