Our previous work confirmed that the higher survival, growth, and commercial performance of a mussel stock collected from a specific lagoon have been maintained over the last 25 years at a microgeographic scale despite intensive transfers of its spat to other local mussel sites. The objective of this study was to identify potential selection mechanisms supporting the quality of this stock. We used a mesocosm approach to examine the effect of maximum seawater temperature measured in the field on the different ontogenic stages of Mytilus edulis to simulate similar patterns in the laboratory. We demonstrated that thermal selection did not affect the development of peri-metamorphic stages (< 1 mm) since no effects were observed on growth, survival, or prodissoconch II size under natural thermal variations. However, our experimental results clearly indicated the existence of a thermal selective pressure (24 °C for 85 h) on 4.5–7 mm juvenile mussels, with growth performance enhanced in surviving individuals. Mortality was 37% higher compared to the control group, suggesting the elimination of more sensitive and less performant mussels. Interestingly, surviving individuals showed improved shell and tissue growth rates, by 22 and 51%, respectively. Our results support the hypothesis that the thermal selection of highly performant stock is size-dependent. The selective pressure demonstrated in this study along with our previous work highlighting the physiological and genetic differences between local stocks constitute the key mechanisms leading to the observed stable production performance over decades at a microgeographic scale.