Understanding the conformation effect on force-induced melting is important for developing advanced semi-crystalline polymer materials. Here, two types of polymer single crystals, polycaprolactone (zigzag conformation) and poly(L-lactic acid) (helical conformation), have been selected to study the conformation effect on force-induced melting by using the atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS). We find that the zigzag chains facilitate the stick-slip motion, and the single helical chain takes smooth motion during force-induced melting from the single crystals. Furthermore, we illustrate that the conformation acts on the force-induced melting by defining the interaction in between the adjacent stems. This SMFS study deepens our understanding on the relationship between the chain conformation and nanomechanical properties of polymer crystals.