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We present a simple and effective way to improve the thermal stability of nano-domains written with an atomic force microscope (AFM)-tip voltage in a lithium niobate film on insulator (LNOI). We show that nano-domains in LNOI (whether in the form of stripe domains or dot domains) degraded, or even disappeared, after a post-poling thermal annealing treatment at a temperature on the order of &#8764;100 <inline-formula> <math display="inline"> <semantics> <msup> <mrow></mrow> <mo>∘</mo> </msup> </semantics> </math> </inline-formula>C. We experimentally confirmed that the thermal stability of nano-domains in LNOI is greatly improved if a pre-heat treatment is carried out for LNOI before the nano-domains are written. This thermal stability improvement of nano-domains is mainly attributed to the generation of a compensating space charge field parallel to the spontaneous polarization of written nano-domains during the pre-heat treatment process.