We present an overview of a deep transient survey of the COSMOS field with the Subaru Hyper Suprime-Cam (HSC). The survey was performed for the 1.77 deg ultra-deep layer and 5.78 deg deep layer in the Subaru Strategic Program over 6- and 4-month periods from 2016 to 2017, respectively. The ultra-deep layer shows a median depth per epoch of 26.4, 26.3, 26.0, 25.6, and 24.6 mag in $g$, $r$, $i$, $z$, and $y$ bands, respectively; the deep layer is $\sim$ 0.6 mag shallower. In total, 1,824 supernova candidates were identified. Based on light curve fitting and derived light curve shape parameter, we classified 433 objects as Type Ia supernovae (SNe); among these candidates, 129 objects have spectroscopic or COSMOS2015 photometric redshifts and 58 objects are located at $z>1$. Our unique dataset doubles the number of Type Ia SNe at $z>1$ and enables various time-domain analyses of Type II SNe, high redshift superluminous SNe, variable stars, and active galactic nuclei.