Microplastics (the term for plastics at sizes of <5 mm) might be introduced into the environment from domestic or agricultural activities or from the breakdown of plastic pieces, particles, and debris that are bigger in size. Their presence in the aquatic environment has caused accumulation problems, as microplastics do not easily break down and can be digested by some aquatic organisms. This study was conducted to screen and monitor the level of microplastic pollution in polychaete worms using pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS). The study was conducted in Setiu Wetlands, Malaysia from November 2015 to January 2017 at five-month intervals and covered all monsoon changes. Results from physical and visual analyses indicated that a total number of 371.4 ± 20.2 items/g microplastics were retrieved from polychaete for all seasons, in which, the majority comprised transparent microplastics (49.87%), followed by brown with 138.3 ± 13.6 items/g (37.24%), 21.7 ± 1.9 items/g for blue (5.84%), and 12.9 ± 1.1 items/g for black (3.47%), while the remaining were green and grey-red colors. Statistical analysis using Kruskal–Wallis showed insignificant differences (p > 0.05) between the sampling station and period for the presence of a microplastics amount. Most of the microplastics were found in fiber form (81.5%), whereas the remaining comprised fragment (18.31%) and film (0.19%) forms. Further analysis with Py-GC/MS under a selective ion monitoring mode indicated that pyrolytic products and fragment ions for a variety of polymers, such as polyvinyl chloride, polypropylene, polyethylene, polyethylene terephthalate, polyamide, and polymethylmethacrylate, were detected. This study provides an insightful application of Py-GC/MS techniques for microplastics monitoring, especially when dealing with analytical amounts of samples.