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Atomically thin layers of transition-metal dicalcogenides (TMDCs) are often known to be metastable in the ambient atmosphere. Understanding the mechanism of degradation is essential for their future applications in nanoelectronics, and thus has attracted intensive interest recently. Here, we demonstrate a systematic study of atomically thin WTe$_{2}$ in its low temperature quantum electronic transport properties. Strikingly, while the temperature dependence of few layered WTe$_{2}$ showed clear metallic tendency in the fresh state, degraded devices first exhibited a re-entrant insulating behavior, and finally entered a fully insulating state. Correspondingly, a crossover from parabolic to linear magnetoresistance, and finally to weak anti-localization was seen. Real-time Raman scattering measurement, together with transmission electron microscopy studies done before and after air degradation of atomically thin WTe$_{2}$ further confirmed that the material gradually form amorphous islands. It thus leads to localized electronic states and explains the low temperature Coulomb gap observed in transport measurements. Our study reveals for the first time the correlation between the unusual magnetotransport and disorder in few-layered WTe$_{2}$, which is indispensable in providing guidance on its future devices application.