Spin-forbidden triplet excited states of conjugated polymers have important ramifications for material performance and stability, yet triplet processes are difficult to understand and control at the bulk material level. We investigate the effect of a heavy heteroatom and chain conformation on triplet-mediated oxygen photochemistry events in poly(3-hexylthiophene) (P3HT) and poly(3-hexylselenophene) (P3HS) systems using high throughput single molecule spectroscopic imaging. Fluorescence intensity transients of both polymers exhibit discrete intermittency behavior (blinking) characteristic of collapsed conformations and efficient energy funneling. Although both systems have similar molecular weights (∼30 kDa), P3HS transients show unexpectedly longer average “on” times and larger average intensities that we attribute to shorter-lived triplets and faster ground electronic state recycling than in P3HT counterparts. This lowers the probability of sensitizing reactive oxygen species and residence times in “off” states. We use detailed statistical modeling incorporating a hidden two-state Markov chain with a transient bleach state to simulate irreversible photobleaching. Statistical distributions of “on” and “off” time distributions from simulated fluorescence intensity transients are in excellent agreement with experiment, consistent with lower average triplet occupancies in P3HS. Our findings offer new molecular-level insights of heavy atom effects on triplet occupancies and discrete photochemistry events that are difficult to resolve at the ensemble level because of averaging over all conformations and packing arrangements.