Chlorella sp. MBFJNU-17 rich in starch and protein could be obtained by modulating the glucose and urea content during its cultivation. Whether MBFJNU-17 was a potential source of starch with adjustable structures was still unclear. In this study, MBFJNU-17 cells with different starch content were collected by regulating glucose (3–15 g/L) and urea content (0–4 g/L) during heterotrophic cultivation. Cells cultured with high glucose content (15 g/L) and low urea content (0 g/L) had a high starch content. Moreover, the starches produced by these cells displayed a larger molar mass and a higher proportion of ordered structures. On the other hand, cells cultured with limited glucose content (3 g/L) and sufficient urea content (0 g/L) showed lower starch content, along with lower molar mass and a reduced amount of ordered structures. Starch granules derived from cells with higher glucose culture conditions demonstrated lower digestibility. Findings suggested that MBFJNU-17 cells with adjustable starch structures and digestibility could be obtained by modulating heterotrophic cultivation conditions.