Watercored apple is a type of fruit with unique flavor and visual appearance. However, the watercore feature of apples will gradually disappear or develop internal disorders during storage, which would compromise their commercial value. In this study, the dissipation of watercore and spread of internal storage disorders (ISD) of the apple were investigated during 120 days preservation at 0°C under the four preservation conditions below: (a) regular air as control; (b) 1-methylcyclopropene (1-MCP) then stored in regular air; (c) at 2.5 kPa O2 plus 2.5 kPa CO2 with pulsed controlled atmosphere (pCA) storage; and (d) with 1-MCP then stored at 2.5 kPa O2 plus 2.5 kPa CO2 with pulsed controlled atmosphere (1-MCP + pCA). Results indicated that the watercore disappeared from the control group faster than that from the treated groups. The 1-MCP + pCA watercore group maintained the highest watercore index and the minimum weight loss, but ISD became significantly serious compared to other treatments at the end of the 120 days storage. Although some ISD occurred in the pCA treatment group, the decreases firmness of pulp and accumulations of malondialdehyde were the least among all four groups. In conclusion, pCA treatment retained larger watercore, less likelihood of ISD, higher firmness, less weight loss than control group, and less browning in comparison to 1-MCP + pCA group after 120 days' storage. The results help us further understand the mechanism of watercore regulation during storage.