The disruption of thyroid hormones because of chemical exposure is a significant societal problem. Chemical evaluations of environmental and human health risks are conventionally based on animal experiments. However, owing to recent breakthroughs in biotechnology, the potential toxicity of chemicals can now be evaluated using 3D cell cultures. In this study, the interactive effects of thyroid‐friendly soft (TS) microspheres on thyroid cell aggregates are elucidated and their potential as a reliable toxicity assessment tool is evaluated. Using state‐of‐the‐art characterization methods coupled with cell‐based analysis and quadrupole time‐of‐flight mass spectrometry, it is shown that TS‐microsphere‐integrated thyroid cell aggregates exhibit improved thyroid function. Specifically, the responses of zebrafish embryos, which are used for thyroid toxicity analysis, and the TS‐microsphere‐integrated cell aggregates to methimazole (MMI), a known thyroid inhibitor, are compared. The results show that the thyroid hormone disruption response of the TS‐microsphere‐integrated thyroid cell aggregates to MMI is more sensitive compared with those of the zebrafish embryos and conventionally formed cell aggregates. This proof‐of‐concept approach can be used to control cellular function in the desired direction and hence evaluate thyroid function. Thus, the proposed TS‐microsphere‐integrated cell aggregates may yield new fundamental insights for advancing in vitro cell‐based research.