Control of spin waves in magnonic crystals is essential for magnon-based computing. Crystals made of ferromagnetic metals offer versatility in band structure design, but strong magnetic damping restricts their transmission efficiency. Yttrium iron garnet (YIG) with ultralow damping is the palpable alternative, yet its small saturation magnetization limits dipolar coupling between discrete units. Here, we experimentally demonstrate low-loss spin-wave manipulation in magnonic crystals of physically separated nanometer-thick YIG stripes. We enhance the transmission of spin waves in allowed minibands by filling the gaps between YIG stripes with CoFeB. Thus-formed magnonic crystals exhibit tunable bandgaps of 50–200 MHz with nearly complete suppression of the spin-wave signal. We also show that Bragg scattering on only two units produces clear frequency gaps in spin-wave transmission spectra. The integration of strong ferromagnets in nanometer-thick YIG-based magnonic crystals provides effective spin-wave manipulation and low-loss propagation, a vital parameter combination for magnonic technologies.