First beam commissioning of SuperKEKB (Phase-1), which is an asymmetry double ring collider of 7-GeV electron and 4-GeV positron beams, which had started from February, has been successfully accomplished at the end of June 2016, and the desired beam current for Phase-1 was achieved in both rings. This paper summarize the operation results related to low level RF (LLRF) control issues during the Phase-1 commissioning, including the system tuning, the coupled bunch instability and the bunch gap transient effect. RF system of SuperKEKB consists of about thirty klystron stations in both rings. Newly developed LLRF control systems were applied to the nine stations among the thirty for Phase-1. The RF reference signal distribution system has been also upgraded for SuperKEKB. These new systems worked well without serious problem and they contributed to smooth progress of the commissioning. The old existing systems, which had been used in the KEKB operation, were still reused for the most stations, and they also worked as soundly as performed in the KEKB operation.