In-group heterogeneity is often neglected during investigations of motor development patterns in children. Moreover, the variation in motor development patterns over time has seldom been examined. In this work, 1884 three-year-old preschoolers were selected from a panel study conducted in Taiwan called the National Longitudinal Study of Child Development and Care. A confirmatory factor analysis was applied to analyze the construct validity of the assessments of motor development used for these children. A latent profile analysis and latent transition analysis (LTA) were sequentially applied to clarify their motor development patterns at the ages of three and four years and their transitions between these two ages. The following findings were obtained: (1) The motor development assessment had good validity. (2) Considerable heterogeneity regarding motor development in preschoolers was observed, in which four and three subgroups displaying distinct levels of mastery with respect to their gross and fine motor skills were identified at the ages of three and four years, respectively. (3) From age three to age four, a large proportion of the preschoolers exhibited improvements or retentions in both gross and fine motor skills, whereas some of the preschoolers were classified into subgroups displaying “gross motor retention and fine motor progression,” “gross motor progression and fine motor retention,” “gross motor retention and fine motor regression,” and “gross motor regression and fine motor progression.” Few preschoolers exhibited “general motor regression.” The present results suggest that there were considerable heterogeneous groups in the motor development in preschoolers in the middle of early childhood, and this phenomenon has rarely been addressed in former studies. The LTA results implied that effective interventions should be given sequentially to preschoolers in subgroups whose motor development presented regression and retention tendencies.