Free-falling microstructure profiler (FFMP) is the most effective platform for measuring ocean microstructure turbulence. Vibration is the key factor of influencing the accuracy of the measurement of the shear sensor mounted on the leading end of the FFMP. In the present work, vibration behavior of an FFMP called FFMP1000 was studied through fluid–structure interaction (FSI) simulations and field trials. Vibration characteristics and mechanism of the FFMP1000 were also discussed. Results showed that motion of the FFMP was like a compound pendulum oscillation, and was caused by vortex shedding at the trailing end of the FFMP. Empirical formulas used to predict the oscillation of the FFMP were deduced based on the characteristics of motion behavior and confirmed through sea trials. The present achievement provides scientific guidance for designing optimal hydrodynamic hull shape of the FFMP. It is also useful to estimate the low end detection limit of the FFMP and to modify the turbulence kinetic energy dissipation rate during ocean observations.