We present simultaneous measurements of emission from dust continuum at 230 GHz and the J=2-1 $^{12}$CO, $^{13}$CO and C$^{18}$O isotopologues at $sim$ 15 pc resolution from individual Giant Molecular Clouds (GMCs) in the Andromeda galaxy (M31). These observations were obtained in an ongoing survey of this galaxy being conducted with the Submillimeter Array (SMA). Initial results describing the continuum and $^{12}$CO emission were published earlier. Here we primarily analyze the observations of $^{13}$CO and C$^{18}$O emission and compare them to the measurements of dust continuum and $^{12}$CO emission. We also report additional dust continuum and CO measurements from newly added GMCs to the M31 sample. We detect spatially resolved $^{13}$CO emission with high signal-to-noise in 31 objects. We find the extent of the $^{13}$CO emission to be nearly comparable to that of $^{12}$CO, typically covering 75% of the area of the $^{12}$CO emission. We derive $^{13}$CO and C$^{18}$O abundances of 2.9 $times 10^{-6}$ and 4.4 $times 10^{-7}$ relative to H$_2$, respectively, by comparison with hydrogen column densities of the same regions derived from the dust continuum observations assuming a Milky Way gas-to-dust ratio. We find the isotopic abundance ratio [$^{13}$CO]/[C$^{18}$O] = 6.7$pm$2.9 to be consistent with the Milky Way value (8.1). Finally, we derive the mass-to-light conversion factors for all three CO species to be $alpha_{12} = 8.7 pm 3.9$, $alpha_{13} = 48.9 pm 20.4$ and $alpha_{18} = 345^{+25}_{-31}$ M$_odot$ (K km s$^{-1}$pc$^2$)$^{-1}$ for the J=2-1 transitions of $^{12}$CO, $^{13}$CO and C$^{18}$O, respectively.
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