This study investigated the effect of small scale enterprise structure on industrial relations in Port Harcourt city, Nigeria. Descriptive survey design was employed and the study essentially utilized the questionnaire survey. In addition, field instrument from observation and personal interview were triangulated with review of relevant literature to cover different scope of the study. A total of 255 questionnaires were administered to the survey respondents from three small scale enterprises and 15 respondents each from five different sectors. Of the 225 questionnaires distributed, 199 usable questionnaires were returned yielding a response rate of 88.44%. The data were analyzed using frequency percentage for descriptive analysis, Pearson’s correlation coefficient (r) to determine the strength of relationship between small scale enterprise structure and industrial relations and chi-square (χ2) for testing the postulated hypothesis. The findings revealed that small scale enterprise structure negatively affects industrial relations because of rigid, one channel communication (downward) and generalized task structure employed by small business enterprises in Port Harcourt city. Based on the findings, it was recommended that small businesses in Port Harcourt city should design enterprise structure that will induce relative flexibility, union formation, specialized task and an ideal relationship of gains, trust and respect. This will invoke harmonious relations for the purposes of production, profitability and sustained benefits.