Development and stability of synchronized long-period stacking ordered (LPSO) structures in Mg97Y2Zn1 alloy were examined by synchrotron-radiation small- and wide-angle scattering/diffraction measurements. The main LPSO structure in the as-cast polycrystalline ingot was 18R, and 14H structure grew at the cost of 18R during annealing. The in-plane peak position increased for longer annealing times in isothermal annealing and also at higher temperatures during in situ heating measurements, and it was interpreted by a composition of peaks corresponding to several sites. The experimental instability temperatures obtained by in situ measurements for in-plane ordering, 18R, and 14H structures agreed within experimental resolution.