We studied the evolution of isolated strange stars (SSs) synthetically, considering the influence of r-mode instability. Our results show that the cooling of SSs with non-ultrastrong magnetic fields is delayed by heating due to r-mode damping for millions of years, while the spin-down of the stars is dominated by gravitational radiation (GR). Especially for the SSs in a possible existing colour-flavour locked (CFL) phase, the effect of r-mode instability on the evolution of stars becomes extremely important because the viscosity, neutrino emissivity and specific heat involving pairing quarks are blocked. It leads to the cooling of these colour superconducting stars being very slow and the stars can remain at high temperature for millions of years, which differs completely from previous understanding. In this case, an SS in CFL phase can be located at the bottom of its r-mode instability window for a long time, but does not spin-down to a very low frequency for hours.
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