Transparent crystals of long afterglow are keenly desired for advanced applications involving three-dimensional information storage and volumetric display. Here, we report the growth of a perovskite crystal, Cs2NaInCl6:Mn, via a facile hydrothermal reaction. The crystal featured a high transparency up to 90% in a broad range from 400 to 750 nm. Upon ultraviolet (UV) excitation, the crystal exhibited an overlapped emission from both self-trapped exciton (STE) and Mn ions. An unusual energy transfer from Mn ion to STE was revealed through steady-state and transient photoluminescence (PL) spectra. Through concentration tuning, the afterglow duration was extended to 2500 s with a signal-to-noise ratio over 20. The single dopant of Mn ions was found to play two roles in afterglow mechanism, including both electron traps and emitting activators. This work provided a facile method to synthesize transparent crystals of persistent luminescence, opening many avenues for three-dimensional information storage and volumetric display.