The performance of organic solar cells has remarkably improved recently, where the cell structures are important for achieving high efficiency and stability. The formation and accumulation of long-lived charges in the cells are critical for the efficiency and stability of the cells; however, their relations with the cell structures have not yet been investigated from a microscopic viewpoint. Here, we show the origin of higher efficiency and stability of inverted organic solar cells compared to those of conventional cells, even though the same photoactive layers with fullerene acceptors are utilized. We directly study the formation and accumulation of long-lived charges in these cells with electron spin resonance (ESR) at a molecular level for as-prepared states and operando states. We find the reduced effects of formation and accumulation of long-lived charges for the efficiency and stability in the inverted cells compared to the case of the conventional cells. These findings are useful for deeply understanding the operation mechanism of organic solar cells as well as further improving their efficiency and stability.