In recent years, the bakery market has grown rapidly. Alongside its growth and fast change, it is very important to comprehend the productivity change of the bakery industry. Nowadays, effective management is more and more important to ensure the sustainable development of enterprises. Thus, productivity change of 22 self-owned stores of a famous bakery company (85 °C) from 2011 to 2016 was quantitatively analyzed and evaluated by adopting Malmquist index model in this study. Based on the Malmquist index model, the overall mean for total productivity change of 85 °C increased slightly from 2011 to 2016, and the productivity change was easily affected by technical progress. Moreover, the results also show that the north-district self-owned stores (which are located in subtropical climate) have the worst technical progress and total factor productivity change during 2011–2016 period by adopting the non-parametric Kruskal–Wallis and Dunn post-hoc test.