In recent years, the reform of compulsory education has been continuously deepened, but the phenomenon of insufficient student motivation remains widespread and tends to affect younger students. This continues to be a significant challenge in the field of education. To effectively improve students’ intellectual development, it is crucial to understand the characteristics and developmental patterns of students’ learning motivation. Based on the situated expectancy-value theory, this study explored the latent transitions of primary school students’ motivation profiles and examined the impact of gender, socio-economic status, and parenting styles on these transitions. The study conducted three rounds of one-year follow-up surveys and found that students’ perceptions of their learning ability, value, and cost could form four typical motivational profiles: the average motivation group, well-adapted group, poorly adapted group, and high-cost group. These profiles generally remained stable over the year, but there were also trajectories of transitions between different profiles. In terms of influencing factors, the results showed that girls exhibited more positive changes in learning motivation, while family economic status did not significantly affect motivational transitions. Furthermore, parental autonomy support positively influenced motivational transitions, whereas parental psychological control had a negative impact. These findings provide a scientific basis for understanding the patterns and developmental trends of primary school students’ learning motivation in China.