Lanthanide-doped upconversion nanocrystals (UCNCs) have recently become an attractive nonlinear fluorescence material for use in bioimaging because of their tunable spectral characteristics and exceptional photostability. Plasmonic materials are often introduced into the vicinity of UCNCs to increase their emission intensity by means of enlarging the absorption cross-section and accelerating the radiative decay rate. Moreover, plasmonic nanostructures (e.g., gold nanorods, GNRs) can also influence the polarization state of the UC fluorescence—an effect that is of fundamental importance for fluorescence polarization-based imaging methods yet has not been discussed previously. To study this effect, we synthesized GNR@SiO2@CaF2:Yb3+,Er3+ hybrid core–shell–satellite nanostructures with precise control over the thickness of the SiO2 shell. We evaluated the shell thickness-dependent plasmonic enhancement of the emission intensity in ensemble and studied the plasmonic modulation of the emission polarization at the single-particle level. The hybrid plasmonic UC nanostructures with an optimal shell thickness exhibit an improved bioimaging performance compared with bare UCNCs, and we observed a polarized nature of the light at both UC emission bands, which stems from the relationship between the excitation polarization and GNR orientation. We used electrodynamic simulations combined with Förster resonance energy transfer theory to fully explain the observed effect. Our results provide extensive insights into how the coherent interaction between the emission dipoles of UCNCs and the plasmonic dipoles of the GNR determines the emission polarization state in various situations and thus open the way to the accurate control of the UC emission anisotropy for a wide range of bioimaging and biosensing applications.