Cell cycle distribution of adherent cells is typically assessed using flow cytometry, which precludes themeasurements of many cell properties and their cycle phase in the same environment. Here we developand validate a microscopy system to quantitatively analyze the cell-cycle phase of thousands ofadherent cells and their associated cell properties simultaneously. This assay demonstrates thatpopulation-averaged cell phenotypes can be written as a linear combination of cell-cycle fractions andphase-dependent phenotypes. By perturbing the cell cycle through inhibition of cell-cycle regulators orchanging nuclear morphology by depletion of structural proteins, our results reveal that cell cycleregulators and structural proteins can significantly interfere with each other’s prima facie functions. Thisstudy introduces a high-throughput method to simultaneously measure the cell cycle and phenotypesat single-cell resolution, which reveals a complex functional interplay between the cell cycle and cellphenotypes.