Holomorphicity of vector bundles can stabilize complex structure moduli of a Calabi-Yau threefold in N = 1 supersymmetric heterotic compactifications. In principle, the Atiyah class determines the stabilized moduli. In this paper, we study how this mechanism works in the context of elliptically fibered Calabi-Yau manifolds where the complex structure moduli space contains two kinds of moduli, those from the base and those from the fibration. Defining the bundle with spectral data, we find three

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... types of situations when bundles' holomorphicity depends on algebraic cycles exist only for special loci in the complex structure moduli, which allows us to stabilize both of these two moduli. We present concrete examples for each type and develop practical tools to analyze the stabilized moduli. Finally, by checking the holomorphicity of the four-flux and/or local Higgs bundle data in F-theory, we briefly study the dual complex structure moduli stabilization scenarios.